[English] 日本語
Yorodumi
- PDB-3ruy: Crystal Structure of the Ornithine-oxo acid transaminase RocD fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ruy
TitleCrystal Structure of the Ornithine-oxo acid transaminase RocD from Bacillus anthracis
ComponentsOrnithine aminotransferase
KeywordsTRANSFERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha and beta protein / PLP-dependent
Function / homology
Function and homology information


ornithine aminotransferase activity / ornithine aminotransferase / L-proline biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Ornithine aminotransferase, bacterial type / Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 ...Ornithine aminotransferase, bacterial type / Ornithine aminotransferase / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ornithine aminotransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Brunzelle, J.S. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of the Ornithine-oxo acid transaminase RocD from Bacillus anthracis
Authors: Anderson, S.M. / Wawrzak, Z. / Brunzelle, J.S. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ornithine aminotransferase
B: Ornithine aminotransferase


Theoretical massNumber of molelcules
Total (without water)86,1442
Polymers86,1442
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint-60 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.120, 98.291, 126.783
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ornithine aminotransferase / OAT / Ornithine-oxo-acid aminotransferase


Mass: 43072.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: rocD, BA_1154, GBAA_1154, BAS1071 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81TV3, ornithine aminotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Sequence detailspyridoxal-5-phosphate covalently bound to lysine 255

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 12.5mM suberic acid, 12.5mM sebacic acid, 12.5mM hexadecanedioic acid, 12.5mM dodecanedioic acid, 40% ethanol, 100mM HEPES, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2011 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionHighest resolution: 2.65 Å / Num. all: 26350 / Num. obs: 25718 / % possible obs: 97.6 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.1 / Redundancy: 5.8 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 27.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2598 / % possible all: 81.6

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→33.98 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7795 / SU ML: 0.82 / σ(F): 1.5 / σ(I): 2.1 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 1268 4.97 %random
Rwork0.1958 ---
all0.1984 26122 --
obs0.1976 25490 97.6 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.835 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 177.09 Å2 / Biso mean: 86.45 Å2 / Biso min: 33.19 Å2
Baniso -1Baniso -2Baniso -3
1--6.4317 Å20 Å2-0 Å2
2--24.7062 Å20 Å2
3----18.2745 Å2
Refinement stepCycle: LAST / Resolution: 2.65→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6005 0 0 84 6089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046127
X-RAY DIFFRACTIONf_angle_d0.7488330
X-RAY DIFFRACTIONf_chiral_restr0.05940
X-RAY DIFFRACTIONf_plane_restr0.0031089
X-RAY DIFFRACTIONf_dihedral_angle_d14.0412258
LS refinement shellResolution: 2.65→2.74 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.364 100 -
Rwork0.319 2253 -
all-2364 -
obs-2104 82.8 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.80080.5936-0.41380.5367-0.06521.58130.2121-0.2356-1.19440.8898-1.6166-0.73750.98581.1208-0.60960.4938-0.0205-0.34231.33180.010.9766-2.766613.415818.4122
20.4489-0.26420.28240.4464-0.28830.4804-0.0573-0.13970.29350.03510.0124-0.31990.4262-0.1867-0.00490.3742-0.0338-0.08210.4502-0.08330.5728-8.344719.90092.53
31.2726-0.4169-0.74850.3260.49260.6884-0.13960.20980.2223-0.3070.36520.27530.4091-1.23140.72110.4273-0.2582-0.15690.69250.03820.397-31.5159.89124.7992
40.72660.23590.60630.4826-0.52013.44210.08160.4497-0.039-0.241-0.14350.32870.44460.7117-0.10680.6465-0.1635-0.11490.413-0.03840.5202-26.1215-0.6074-5.7945
51.7031-0.5523-0.6130.72730.88791.6911-0.1708-0.295-0.6727-0.48030.1803-0.32670.79870.57170.0251.0268-0.02-0.06470.37060.01240.8241-13.0701-14.7487-0.7237
60.3877-0.4139-0.17630.3367-0.01271.3779-0.0640.12-0.3374-0.0598-0.2775-1.14910.50531.7806-0.00680.98580.3002-0.07440.6427-0.02530.8889-2.1033-11.71494.3446
72.05970.19250.24790.7881-0.14130.1926-0.12810.8208-0.2015-0.52510.243-0.01160.81930.58570.02120.92350.07960.02030.4192-0.16320.556-8.7699-6.9623-12.0383
81.2912-0.4640.2170.57040.28520.38320.1539-0.7205-0.4848-0.02650.146-0.83560.8174-0.0251-0.03670.7697-0.0503-0.03120.3153-0.0290.5375-20.5238-1.4812-2.4115
92.20160.75230.3141.53790.29113.2955-0.37950.6154-0.4577-0.21320.2392-0.14730.6978-0.0996-0.01080.42370.0644-0.0460.2265-0.05180.4492-8.22968.8311-7.6296
100.3027-0.19530.23720.27860.08390.2527-0.1007-0.44430.04740.66720.716-0.36340.94110.268-00.64810.1203-0.11030.65070.09410.60256.679513.38052.0431
110.61320.7240.14580.8189-0.05830.5774-0.46430.17620.1755-0.54820.41-0.36590.0412-0.65580.00620.381-0.0067-0.0090.4433-0.04820.58340.824219.8795-7.6435
120.36490.0006-0.45270.20970.47481.3385-0.82351.4547-1.2021-0.48-0.118-0.08250.48971.3987-0.16420.9399-0.5294-0.12471.3814-0.23690.7717-37.6103-2.9817-0.5479
130.88360.2519-0.21531.52580.25621.9763-0.0847-0.11080.1741-0.01110.15160.22240.1355-0.37480.00240.3715-0.1203-0.03550.70520.05080.4844-29.105410.933713.9788
141.92360.3621-0.33930.80570.04531.1306-0.3271-0.6804-0.0153-0.10050.5618-0.07270.4233-0.04460.18830.6279-0.0205-0.140.47260.27130.4052-10.7768-5.767921.0914
151.15960.14660.38890.0187-0.12641.5178-0.2908-0.7142-1.20360.3920.24520.46251.0306-0.7754-0.06451.0605-0.1407-0.10230.55490.36590.9557-19.4738-19.23914.6926
160.81860.8511-0.28560.83720.34950.823-0.0952-0.5525-0.32630.50950.0364-0.20030.6466-0.1406-0.27820.8676-0.0098-0.09840.83180.30770.5862-17.9914-7.69528.3786
170.34560.564-0.31911.1341-0.82370.65720.2401-0.98510.1286-0.0596-0.1968-0.38770.19741.22230.00190.4115-0.0153-0.11430.67380.10270.406-16.20058.767718.8089
180.8583-0.84210.02311.8791-0.77041.60650.2704-0.7163-0.22120.228-0.07260.81970.2828-1.13330.14690.6995-0.45420.01251.08220.3530.7699-43.1663-5.342925.7049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:27)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 28:58)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 59:83)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 84:105)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 106:145)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 146:175)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 176:253)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 254:276)A0
9X-RAY DIFFRACTION9chain 'A' and (resseq 277:349)A0
10X-RAY DIFFRACTION10chain 'A' and (resseq 350:369)A0
11X-RAY DIFFRACTION11chain 'A' and (resseq 370:396)A0
12X-RAY DIFFRACTION12chain 'B' and (resseq 3:27)B0
13X-RAY DIFFRACTION13chain 'B' and (resseq 28:83)B0
14X-RAY DIFFRACTION14chain 'B' and (resseq 84:145)B0
15X-RAY DIFFRACTION15chain 'B' and (resseq 146:175)B0
16X-RAY DIFFRACTION16chain 'B' and (resseq 176:276)B0
17X-RAY DIFFRACTION17chain 'B' and (resseq 277:307)B0
18X-RAY DIFFRACTION18chain 'B' and (resseq 308:396)B0

+
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://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