Structure of decorbin-binding protein A from Borrelia burgdorferi
SAGLTGATKI RLERSAKDIT DEIDAIKKDA ALKGVNFDAF KDKKTGSGVS ENPFILEAKV RATTVAEKFV IAIEEEATKL KETGSSGEFS AMYDLMFEVS KPLQKLGIQE MTKTVSDAAE ENPPTTAQGV LEIAKKMREK LQRVHTKNYC TLKKKENSTF TDEKCKNNSA GLTGATKIRL ERSAKDITDE IDAIKKDAAL KGVNFDAFKD KKTGSGVSEN PFILEAKVRA TTVAEKFVIA IEEEATKLKE TGSSGEFSAM YDLMFEVSKP LQKLGIQEMT KTVSDAAEEN PPTTAQGVLE IAKKMREKLQ RVHTKNYCTL KKKENSTFTD EKCKNN
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | disulfide | sing | 1:CYS150:SG | 1:CYS165:SG |
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 50.2 % (1956 of 3896) | 48.7 % (993 of 2038) | 50.5 % (762 of 1508) | 57.4 % (201 of 350) |
Backbone | 57.7 % (1154 of 2000) | 58.7 % (400 of 682) | 56.1 % (555 of 990) | 60.7 % (199 of 328) |
Sidechain | 44.8 % (991 of 2214) | 43.7 % (593 of 1356) | 47.4 % (396 of 836) | 9.1 % (2 of 22) |
Aromatic | 20.6 % (37 of 180) | 22.2 % (20 of 90) | 18.9 % (17 of 90) | |
Methyl | 58.5 % (213 of 364) | 60.4 % (110 of 182) | 56.6 % (103 of 182) |
1. DBPA
SAGLTGATKI RLERSAKDIT DEIDAIKKDA ALKGVNFDAF KDKKTGSGVS ENPFILEAKV RATTVAEKFV IAIEEEATKL KETGSSGEFS AMYDLMFEVS KPLQKLGIQE MTKTVSDAAE ENPPTTAQGV LEIAKKMREK LQRVHTKNYC TLKKKENSTF TDEKCKNNSA GLTGATKIRL ERSAKDITDE IDAIKKDAAL KGVNFDAFKD KKTGSGVSEN PFILEAKVRA TTVAEKFVIA IEEEATKLKE TGSSGEFSAM YDLMFEVSKP LQKLGIQEMT KTVSDAAEEN PPTTAQGVLE IAKKMREKLQ RVHTKNYCTL KKKENSTFTD EKCKNNSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details anisotropic sample in 5% neutral gel
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
6 | sodium phosphate | natural abundance | 50 mM | |
7 | D2O | natural abundance | 10 % | |
8 | H2O | natural abundance | 90 % | |
9 | polyacrylamide | natural abundance | 5 % |
Pressure 1 atm, Temperature 298 K, pH 6.5
Experiment name J-modulated 15N HSQC, JNC-modulated 15N HSQC
List #2 NCO_RDC, RDC code DNC, Field strength (1H) 800 MHz
Agilent Inova 800 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent Inova 800 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent Inova 800 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent Inova 800 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent Inova 800 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent Inova 800 - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details isotropic sample
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
2 | sodium phosphate | natural abundance | 50 mM | |
3 | D2O | natural abundance | 10 % | |
4 | H2O | natural abundance | 90 % |
Agilent Inova 800 - 800 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details anisotropic sample in 5% neutral gel
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
6 | sodium phosphate | natural abundance | 50 mM | |
7 | D2O | natural abundance | 10 % | |
8 | H2O | natural abundance | 90 % | |
9 | polyacrylamide | natural abundance | 5 % |
Agilent Inova 800 - 800 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details anisotropic sample in 5% neutral gel
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
5 | DBPA | [U-100% 13C; U-100% 15N] | 0.8 mM | |
6 | sodium phosphate | natural abundance | 50 mM | |
7 | D2O | natural abundance | 10 % | |
8 | H2O | natural abundance | 90 % | |
9 | polyacrylamide | natural abundance | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_18329_2lqu.nef |
Input source #2: Coordindates | 2lqu.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
Whether the assembly has a other bond | None |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Ã…) |
---|---|---|---|---|
A:173:CYS:SG | A:188:CYS:SG | oxidized, CA 58.4, CB 38.6 ppm | unknown | 2.021 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
NoneNon-standard residues
NoneSequence alignments
-----30--------40--------50--------60--------70--------80--------90-------100-------110-------120--- SAGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SAGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ----130-------140-------150-------160-------170-------180-------190- KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDEKCKNN |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDEKCKNN -------110-------120-------130-------140-------150-------160--------
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 168 | 0 | 0 | 100.0 |
Content subtype: combined_18329_2lqu.nef
Assigned chemical shifts
-----30--------40--------50--------60--------70--------80--------90-------100-------110-------120--- SAGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .AGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS ----130-------140-------150-------160-------170-------180-------190- KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDEKCKNN ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDE..KNN
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 1019 | 746 | 73.2 |
13C chemical shifts | 754 | 633 | 84.0 |
15N chemical shifts | 180 | 156 | 86.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 341 | 323 | 94.7 |
13C chemical shifts | 336 | 311 | 92.6 |
15N chemical shifts | 164 | 156 | 95.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 678 | 423 | 62.4 |
13C chemical shifts | 418 | 322 | 77.0 |
15N chemical shifts | 16 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 95 | 95 | 100.0 |
13C chemical shifts | 95 | 93 | 97.9 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 45 | 22 | 48.9 |
13C chemical shifts | 45 | 17 | 37.8 |
Covalent bonds
Distance restraints
-----30--------40--------50--------60--------70--------80--------90-------100-------110-------120--- SAGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS |||| ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||| ||||||||||||||| .AGLT.ATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKT..GVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETG.SGEFSAMYDLMFEVS ----130-------140-------150-------160-------170-------180-------190- KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDEKCKNN ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDE..KNN
Dihedral angle restraints
-----30--------40--------50--------60--------70--------80--------90-------100-------110-------120--- SAGLTGATKIRLERSAKDITDEIDAIKKDAALKGVNFDAFKDKKTGSGVSENPFILEAKVRATTVAEKFVIAIEEEATKLKETGSSGEFSAMYDLMFEVS |||||||||||||||||||||||||| |||||||||||||||||||||||||||| ||||||||||||||| ......ATKIRLERSAKDITDEIDAIKKDAAL....................PFILEAKVRATTVAEKFVIAIEEEATKL.....SGEFSAMYDLMFEVS -----30--------40--------50--------60--------70--------80--------90-------100-------110-------120--- ----130-------140-------150-------160-------170-------180-------190- KPLQKLGIQEMTKTVSDAAEENPPTTAQGVLEIAKKMREKLQRVHTKNYCTLKKKENSTFTDEKCKNN |||||| ||||||||||| |||||||||||||||||||||||||||||||| KPLQKL...EMTKTVSDAAE.....TAQGVLEIAKKMREKLQRVHTKNYCTLKKKEN ----130-------140-------150-------160-------170-------180