[English] 日本語
Yorodumi
- PDB-4z9n: ABC transporter / periplasmic binding protein from Brucella ovis ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z9n
TitleABC transporter / periplasmic binding protein from Brucella ovis with glutathione bound
ComponentsAmino acid ABC transporter, periplasmic amino acid-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter / glutathione / GSH / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyBacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / GLUTATHIONE / Amino acid ABC transporter, periplasmic amino acid-binding protein / Amino acid ABC transporter, periplasmic amino acid-binding protein
Function and homology information
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.745 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: ABC transporter / periplasmic binding protein from Brucella ovis with glutathione bound
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amino acid ABC transporter, periplasmic amino acid-binding protein
B: Amino acid ABC transporter, periplasmic amino acid-binding protein
C: Amino acid ABC transporter, periplasmic amino acid-binding protein
D: Amino acid ABC transporter, periplasmic amino acid-binding protein
E: Amino acid ABC transporter, periplasmic amino acid-binding protein
F: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,26426
Polymers215,7866
Non-polymers2,47820
Water34,2101899
1
A: Amino acid ABC transporter, periplasmic amino acid-binding protein
D: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7759
Polymers71,9292
Non-polymers8477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-49 kcal/mol
Surface area22410 Å2
MethodPISA
2
B: Amino acid ABC transporter, periplasmic amino acid-binding protein
E: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7759
Polymers71,9292
Non-polymers8477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-51 kcal/mol
Surface area22780 Å2
MethodPISA
3
C: Amino acid ABC transporter, periplasmic amino acid-binding protein
F: Amino acid ABC transporter, periplasmic amino acid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7138
Polymers71,9292
Non-polymers7856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-44 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.990, 76.930, 131.470
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Amino acid ABC transporter, periplasmic amino acid-binding protein


Mass: 35964.316 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria)
Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: BOV_0736 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VPS6, UniProt: A0A0M3KL33*PLUS
#2: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1899 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MCSG1b2: 25% PEG3350, 0.2M NaCl, 0.1M BisTris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.745→50 Å / Num. obs: 187580 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rsym value: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 1.745→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: phased from iodided soak

Resolution: 1.745→31.655 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 3931 2.1 %Random
Rwork0.1517 ---
obs0.1524 187476 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.745→31.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14578 0 158 1899 16635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815224
X-RAY DIFFRACTIONf_angle_d1.12820712
X-RAY DIFFRACTIONf_dihedral_angle_d12.5585402
X-RAY DIFFRACTIONf_chiral_restr0.0552301
X-RAY DIFFRACTIONf_plane_restr0.0052753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.745-1.76620.2608960.23235291X-RAY DIFFRACTION80
1.7662-1.78860.23391350.2176633X-RAY DIFFRACTION100
1.7886-1.81210.26881450.21076582X-RAY DIFFRACTION100
1.8121-1.8370.23021610.2026606X-RAY DIFFRACTION100
1.837-1.86320.24361320.1876546X-RAY DIFFRACTION100
1.8632-1.8910.21921380.18316621X-RAY DIFFRACTION100
1.891-1.92050.2051530.1836602X-RAY DIFFRACTION100
1.9205-1.9520.20421440.18116594X-RAY DIFFRACTION100
1.952-1.98570.19531190.17346582X-RAY DIFFRACTION100
1.9857-2.02180.17871540.16156624X-RAY DIFFRACTION100
2.0218-2.06070.19711670.15646554X-RAY DIFFRACTION99
2.0607-2.10270.17251260.15246539X-RAY DIFFRACTION100
2.1027-2.14840.16561250.15126664X-RAY DIFFRACTION99
2.1484-2.19840.2021500.15516558X-RAY DIFFRACTION99
2.1984-2.25340.17241480.15336573X-RAY DIFFRACTION99
2.2534-2.31430.21011390.15146564X-RAY DIFFRACTION99
2.3143-2.38230.16481440.14636604X-RAY DIFFRACTION99
2.3823-2.45920.20051420.14856509X-RAY DIFFRACTION99
2.4592-2.54710.17541280.14916595X-RAY DIFFRACTION99
2.5471-2.6490.17511500.15686528X-RAY DIFFRACTION99
2.649-2.76950.20291420.15226588X-RAY DIFFRACTION99
2.7695-2.91540.2031360.15336534X-RAY DIFFRACTION99
2.9154-3.09790.17621430.15486620X-RAY DIFFRACTION99
3.0979-3.33690.16941450.15156640X-RAY DIFFRACTION100
3.3369-3.67220.1551470.13936653X-RAY DIFFRACTION100
3.6722-4.20260.15441370.12216676X-RAY DIFFRACTION100
4.2026-5.29080.16821440.1186728X-RAY DIFFRACTION100
5.2908-31.65970.16471410.14676737X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7726-1.1803-0.16383.6502-0.18772.4876-0.3008-0.1554-0.19930.58740.1110.23290.3885-0.04020.17890.2467-0.02150.06480.16670.02510.123149.05727.363156.3527
20.6365-0.4123-0.19272.1575-0.08371.0218-0.1312-0.15980.04520.35090.0834-0.04630.0362-0.03440.04170.1210.02-0.02490.1562-0.01370.094649.883223.612556.1459
33.00611.0935-1.65214.632-2.55475.2553-0.0424-0.26270.3770.59260.0421-0.1331-0.46390.06270.00220.17850.0506-0.08710.1866-0.07610.20748.835339.106658.2568
43.291-0.442-0.10594.42591.39781.246-0.1004-0.20120.04590.49010.02620.16320.1099-0.19090.0620.16230.0650.01450.19920.01270.105537.906130.015757.9884
51.1494-0.9212-0.27482.21160.45181.3589-0.08040.0311-0.08440.1215-0.01680.06370.1435-0.12820.0990.0487-0.0330.02050.12290.01780.077549.548914.689345.0805
65.537-0.61412.59113.8102-0.08626.23430.10970.5873-0.5621-0.128-0.0981-0.08340.85380.269-0.01650.19820.00070.05750.145-0.05190.205358.496-3.036536.0694
71.3282-0.8002-0.56342.48870.31571.52220.01550.117-0.0643-0.0332-0.11870.20040.1105-0.30420.09570.0723-0.0262-0.02070.1528-0.01550.101846.78812.329140.1104
82.46560.07670.66591.93681.29411.67560.0665-0.19710.04380.10270.1881-0.287-0.14490.4557-0.19950.1086-0.0585-0.01030.2114-0.06760.1827129.062461.201839.0715
90.8956-0.1647-0.41261.44210.64751.7580.02640.0915-0.0225-0.19730.0075-0.0817-0.08830.0978-0.02570.06870.00150.00020.0991-0.01380.1059118.387650.493124.2285
101.662-0.34370.28642.1588-0.39581.53460.0268-0.3130.32910.37920.1027-0.0411-0.47670.1634-0.11070.2549-0.06740.04610.1837-0.07980.163115.170772.35348.5857
111.41640.0141-0.33551.61440.86761.87730.1678-0.01330.1912-0.054-0.0271-0.0666-0.4160.0437-0.10910.1685-0.01880.00930.0701-0.01260.1099113.080969.017235.3231
122.20240.52240.50131.8196-0.75211.13270.0993-0.3988-0.36010.27070.10490.14720.3417-0.4156-0.1870.2599-0.044-0.00160.28350.12460.20365.134248.907519.9473
131.25680.24670.12191.2112-0.30651.4120.0818-0.1739-0.18310.14090.019-0.04110.238-0.1059-0.0870.18370.0248-0.03590.14550.05160.113477.276354.019416.1252
141.11240.27660.41930.66890.20021.5244-0.0087-0.1195-0.06150.03350.0347-0.0658-0.04270.0438-0.03080.14170.0359-0.02150.12010.03040.122486.541563.05120.2469
152.085-0.97530.02032.95120.29891.84080.0694-0.1731-0.33510.0145-0.00330.4730.2236-0.562-0.05030.1765-0.0761-0.01410.31580.06590.183952.929854.61834.6981
161.54950.31370.59431.19030.26341.9252-0.048-0.2529-0.02630.09240.05260.11620.0088-0.36060.00150.09710.0287-0.00160.19180.04030.109162.173663.095410.5678
172.1057-0.04150.93631.14881.0371.557-0.0005-0.01080.121-0.04120.2159-0.5543-0.19060.3079-0.1920.1057-0.03570.050.196-0.00620.502781.14724.29137.3243
181.4410.8125-0.11830.6114-0.04411.0163-0.0088-0.10970.06380.00530.0339-0.52540.1050.2583-0.03360.09010.02110.00470.16020.01060.333976.938313.982537.6369
191.3088-0.0819-0.54181.92020.75151.28830.10410.39470.0935-0.5639-0.078-0.1745-0.1748-0.1619-0.01170.23940.06930.04860.22770.05950.160765.702811.255915.7308
205.2868-0.09211.79173.07971.7694.59060.12240.1862-0.1832-0.2049-0.1492-0.15990.1161-0.240.00510.1630.04330.03590.14160.03130.115866.28861.965519.2395
211.0499-0.0847-0.44551.33560.46341.58730.06530.27990.2576-0.4147-0.0855-0.4096-0.0870.0382-0.01120.20650.05990.12120.20260.11230.276670.612715.127620.0372
222.3809-0.60820.46171.7242-0.45252.79240.0487-0.11550.39580.06760.0346-0.3084-0.35310.1168-0.0950.1196-0.020.0250.1333-0.01370.302567.853133.244242.7586
235.2076-3.26411.81514.0158-2.9163.1413-0.1986-0.45680.79750.52840.221-0.7155-0.54770.042-0.01580.2399-0.0237-0.02550.1865-0.10130.371367.277437.658852.1085
241.24070.0184-0.27691.28770.85042.18280.09670.11030.3426-0.2378-0.0025-0.3106-0.3198-0.0128-0.08610.15110.02730.04040.10480.05590.281765.30631.003434.0158
251.14490.1006-0.64612.03830.01092.0315-0.0106-0.2117-0.05510.3666-0.01280.17550.0806-0.01880.02670.15780.00910.04030.13050.00080.096297.372352.26356.0595
261.506-0.1657-0.80251.60280.54331.68830.2022-0.13080.34140.2361-0.07970.2067-0.4127-0.1774-0.10050.27780.03310.09440.159-0.03020.198291.3969.329756.9917
272.808-0.22480.35251.41260.16733.0424-0.0830.2127-0.45230.0420.02540.08750.47510.04420.04020.1416-0.00890.04650.0878-0.02010.1689102.290839.225837.28
281.6189-0.0853-1.17731.88820.52152.2176-0.01830.098-0.07020.0362-0.02990.25040.0315-0.25960.04390.0572-0.0028-0.02060.1042-0.01360.105294.148850.104339.7511
291.4916-1.8289-0.07282.4128-0.26410.89060.0577-0.0515-0.3217-0.084-0.0365-0.02070.44610.3055-0.01990.41090.0723-0.01560.1809-0.01430.256479.307841.3218-15.6098
301.028-0.19550.27791.6599-0.30340.30890.13120.2434-0.1753-0.354-0.0824-0.02470.50420.1355-0.02490.32250.0361-0.00560.1869-0.0260.111674.506151.3071-21.1851
310.9591-0.5097-0.46931.7296-0.46630.7657-0.02670.0089-0.2631-0.08180.03210.07480.5255-0.07680.10460.2832-0.0174-0.04510.11760.00160.150565.830247.9092-9.988
321.44730.02720.83691.24650.04581.7538-0.10110.05510.1669-0.08550.04930.2565-0.1729-0.28890.09040.1480.0061-0.03070.17910.01410.151554.739267.5094-19.0747
331.0602-0.6428-1.09182.27150.38614.08040.02440.0995-0.2257-0.0225-0.08430.48970.0718-0.66980.07510.1451-0.0646-0.03790.27760.00790.238247.820460.7909-15.7309
342.448-0.60741.09881.2469-0.05793.2394-0.02850.3002-0.0812-0.22190.05880.17480.257-0.1923-0.01770.1487-0.0315-0.04440.14520.00140.129957.746264.1743-26.1232
351.1725-0.48370.21981.0270.361.3167-0.07070.09540.04470.0002-0.0166-0.0529-0.0124-0.08430.03660.1238-0.0377-0.02550.12790.00080.096163.045161.813-15.8737
360.99160.50760.44133.0895-0.14582.27910.09690.0867-0.119-0.0442-0.0999-0.25260.19660.3395-0.07280.13910.0693-0.01380.18650.01280.107485.955857.9295-6.8831
370.61820.8789-0.07047.25660.04680.78070.07740.0397-0.29890.44750.0099-0.71260.31710.4768-0.14690.22540.0937-0.02210.31310.02540.241793.951453.8569-0.8776
380.8696-0.34780.4131.1569-0.28491.5084-0.0174-0.0058-0.0355-0.0328-0.0122-0.12540.15130.18840.02030.09790.0151-0.0060.11890.00610.092979.618664.2067-10.0135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 158 )
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 246 )
6X-RAY DIFFRACTION6chain 'A' and (resid 247 through 273 )
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 321 )
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 50 )
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 215 through 273 )
11X-RAY DIFFRACTION11chain 'B' and (resid 274 through 321 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 50 )
13X-RAY DIFFRACTION13chain 'C' and (resid 51 through 119 )
14X-RAY DIFFRACTION14chain 'C' and (resid 120 through 214 )
15X-RAY DIFFRACTION15chain 'C' and (resid 215 through 273 )
16X-RAY DIFFRACTION16chain 'C' and (resid 274 through 321 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 50 )
18X-RAY DIFFRACTION18chain 'D' and (resid 51 through 98 )
19X-RAY DIFFRACTION19chain 'D' and (resid 99 through 134 )
20X-RAY DIFFRACTION20chain 'D' and (resid 135 through 158 )
21X-RAY DIFFRACTION21chain 'D' and (resid 159 through 214 )
22X-RAY DIFFRACTION22chain 'D' and (resid 215 through 246 )
23X-RAY DIFFRACTION23chain 'D' and (resid 247 through 273 )
24X-RAY DIFFRACTION24chain 'D' and (resid 274 through 321 )
25X-RAY DIFFRACTION25chain 'E' and (resid 2 through 119 )
26X-RAY DIFFRACTION26chain 'E' and (resid 120 through 214 )
27X-RAY DIFFRACTION27chain 'E' and (resid 215 through 273 )
28X-RAY DIFFRACTION28chain 'E' and (resid 274 through 321 )
29X-RAY DIFFRACTION29chain 'F' and (resid 1 through 19 )
30X-RAY DIFFRACTION30chain 'F' and (resid 20 through 71 )
31X-RAY DIFFRACTION31chain 'F' and (resid 72 through 98 )
32X-RAY DIFFRACTION32chain 'F' and (resid 99 through 134 )
33X-RAY DIFFRACTION33chain 'F' and (resid 135 through 158 )
34X-RAY DIFFRACTION34chain 'F' and (resid 159 through 187 )
35X-RAY DIFFRACTION35chain 'F' and (resid 188 through 214 )
36X-RAY DIFFRACTION36chain 'F' and (resid 215 through 246 )
37X-RAY DIFFRACTION37chain 'F' and (resid 247 through 273 )
38X-RAY DIFFRACTION38chain 'F' and (resid 274 through 321 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more