[English] 日本語
Yorodumi
- PDB-4tm5: X-ray crystal structure of a D-amino acid aminotransferase from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tm5
TitleX-ray crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264 bound to the co-factor pyridoxal phosphate
ComponentsD-amino acid aminotransferase
KeywordsTRANSFERASE / D-amino acid / aminotransferase / PLP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


transaminase activity / metal ion binding
Similarity search - Function
Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel ...Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-amino acid aminotransferase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.603 Å
AuthorsFairman, J.W. / Taylor, B.M. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: X-ray crystal structure of a D-amino acid aminotransferase from Burkholderia thailandensis E264 bound to the co-factor pyridoxal phosphate
Authors: Fairman, J.W. / Taylor, B.M. / Edwards, T.E. / Lorimer, D.
History
DepositionMay 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _citation.journal_id_CSD / _entity.formula_weight / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-amino acid aminotransferase


Theoretical massNumber of molelcules
Total (without water)34,2421
Polymers34,2421
Non-polymers00
Water6,287349
1
A: D-amino acid aminotransferase

A: D-amino acid aminotransferase


Theoretical massNumber of molelcules
Total (without water)68,4842
Polymers68,4842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4500 Å2
ΔGint-37 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.830, 70.020, 140.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-416-

HOH

Detailsbiological unit is the same as asym.

-
Components

#1: Protein D-amino acid aminotransferase


Mass: 34241.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I0381 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2T1L0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 400 nl of protein + 400 nl of Morpheus condition C4 - 0.1 M MES/imidazole pH 6.5, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 30 mM sodium nitrate, 30 mM disodium hydrogen phosphate, 30 mM ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12709 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 40085 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.84 % / Biso Wilson estimate: 14.78 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.051 / Χ2: 0.983 / Net I/σ(I): 25.61 / Num. measured all: 234322
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.643.860.8520.4023.2410519291327200.46293.4
1.64-1.690.9220.3654.6615794288328820.403100
1.69-1.740.9560.2866.2616949281728170.314100
1.74-1.790.9720.2317.7616428271227120.253100
1.79-1.850.980.1829.6815920263426330.2100
1.85-1.920.9890.13812.6815421253725370.151100
1.92-1.990.9940.117.0615061247824780.11100
1.99-2.070.9960.08120.6314387237023680.08899.9
2.07-2.160.9980.06525.2113818226822660.07199.9
2.16-2.270.9980.05927.6713356219621950.064100
2.27-2.390.9980.0543012633207620760.06100
2.39-2.530.9980.04734.112031197619760.052100
2.53-2.710.9990.0438.5711340186718660.04499.9
2.71-2.930.9990.03443.7810577175217510.03799.9
2.93-3.20.9990.02951.489494158315800.03299.8
3.2-3.580.9990.02559.38744147014690.02899.9
3.58-4.140.9990.02365.347474129512870.02599.4
4.14-5.0710.0270.036584111411080.02299.5
5.07-7.1710.02164.8550968698570.02498.6
7.170.9990.01869.0326965305070.0295.7

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementResolution: 1.603→46.347 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 2024 5.05 %RANDOM
Rwork0.1539 38020 --
obs0.1557 40044 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.35 Å2 / Biso mean: 19.693 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 1.603→46.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 0 349 2602
Biso mean---30.68 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092353
X-RAY DIFFRACTIONf_angle_d1.2883221
X-RAY DIFFRACTIONf_chiral_restr0.056367
X-RAY DIFFRACTIONf_plane_restr0.006428
X-RAY DIFFRACTIONf_dihedral_angle_d13.446873
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.603-1.64260.26331190.21082501262093
1.6426-1.6870.21971590.185826952854100
1.687-1.73670.20261510.16227132864100
1.7367-1.79270.20411600.157926882848100
1.7927-1.85680.20451560.157526802836100
1.8568-1.93110.19861430.153827092852100
1.9311-2.0190.19831510.154227112862100
2.019-2.12550.19921230.148427432866100
2.1255-2.25860.19571380.145627052843100
2.2586-2.4330.18671340.155627592893100
2.433-2.67780.16421300.160127572887100
2.6778-3.06520.18041510.160527422893100
3.0652-3.86160.17971570.145727682925100
3.8616-46.36620.18811520.14382849300198
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)
11.98690.2216-0.35272.49970.17784.41530.0185-0.04450.0054-0.11370.04350.36940.1816-0.5678-0.12120.1062-0.0291-0.01340.197-0.01870.2151-17.501926.556964.0706
20.86870.07310.01861.18481.14652.7382-0.03210.0984-0.0438-0.0590.01320.0710.0901-0.16280.02230.0887-0.03060.00150.08040.00980.0929-5.890125.601161.0784
30.88070.83870.28561.99941.84982.83930.0598-0.0716-0.13670.17110.0387-0.03830.32750.0492-0.0920.14770.01310.00190.07250.01210.13621.026617.051266.7098
41.30810.08140.61450.477-0.22912.2958-0.04750.0702-0.0396-0.0282-0.02880.09350.0232-0.16460.06150.0934-0.01990.01170.0814-0.0190.1266-8.172322.996861.9543
51.40460.4723-0.43680.5150.21961.2017-0.06190.14120.0048-0.07410.04040.0163-0.0492-0.04640.00550.1295-0.0031-0.01470.07860.00680.10240.915530.137353.9263
61.09590.4409-0.330.9369-0.01831.2726-0.00410.06870.00170.03740.0178-0.0641-0.11090.1471-0.01740.101-0.0206-0.00450.092-0.01190.094711.528534.801459.9236
72.74530.1458-0.65992.2-0.3411.9060.1173-0.3586-0.18570.070.0133-0.4270.28230.7120.04330.13040.00080.00850.2153-0.03450.194919.026523.791854.0649
81.11870.2055-0.45080.9221-0.05651.7472-0.13260.022-0.379-0.08920.1066-0.4080.25390.3340.00630.14080.00350.03690.1802-0.0560.231817.583623.00649.1474
91.49180.9468-0.68771.03880.00571.0871-0.21380.482-0.0356-0.41650.3357-0.2007-0.26360.1428-0.04120.195-0.09610.03860.2145-0.0120.126215.72534.467842.1912
101.1348-1.3417-0.02591.77080.79653.2885-0.16740.3575-0.4759-0.20160.13080.0970.4301-0.30240.08330.258-0.05870.04450.222-0.11610.2036.779116.808241.9073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 25 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 58 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 80 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 122 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 155 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 201 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 202 through 223 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 224 through 263 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 264 through 282 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 283 through 301 )A0

+
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