[English] 日本語
Yorodumi
- PDB-4xa8: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xa8
TitleCrystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homologyD-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
Function and homology information
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHanding, K.B. / Gasiorowska, O.A. / Shabalin, I.G. / Cymborowski, M.T. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: to be published
Title: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2.
Authors: Handing, K.B. / Gasiorowska, O.A. / Shabalin, I.G. / Cymborowski, M.T. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionDec 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)34,7101
Polymers34,7101
Non-polymers00
Water3,117173
1
A: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding

A: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)69,4202
Polymers69,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4630 Å2
ΔGint-34 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.762, 63.714, 154.967
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-426-

HOH

Detailsbiological unit is the same as asym.

-
Components

#1: Protein D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding


Mass: 34709.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: ATCC BAA-1158 / Py2 / Gene: Xaut_2571 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: A7IIH0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.95 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 UL OF 11 MG/ML PROTEIN IN 20 MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 0.1% SODIUM AZIDE, 0.5 MM TCEP and 10 mM NADH WERE MIXED WITH 0.2 UL OF THE TOP96 CONDITION #34 (0.2M MAGNESIUM ...Details: 0.2 UL OF 11 MG/ML PROTEIN IN 20 MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 0.1% SODIUM AZIDE, 0.5 MM TCEP and 10 mM NADH WERE MIXED WITH 0.2 UL OF THE TOP96 CONDITION #34 (0.2M MAGNESIUM CHLORIDE, 6-HYDRATE, 0.1M HEPES, 25%W/V PEG 3350 PH=7.5) AND EQUILIBRATED AGAINST 1.5 M NACL SOLUTION IN 96 WELL 3 DROP CRYSTALLIZATION PLATE (SWISSCI). BEFORE CRYSTALLIZATION PROTEIN WAS INCUBATED WITH 1/50 V/V OF 1 MG/ML TEV SOLUTION AT 289 K FOR 1 HOUR

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22335 / % possible obs: 95.2 % / Redundancy: 9 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Rrim(I) all: 0.073 / Χ2: 1.392 / Net I/av σ(I): 36.413 / Net I/σ(I): 21.738 / Num. measured all: 201327
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.939.60.8352.611100.7860.2760.8810.7596.9
1.93-1.979.40.71411140.8340.2370.7540.76293.9
1.97-2.019.50.57110780.8750.190.6030.81795.1
2.01-2.059.40.50411150.9070.1680.5320.84996
2.05-2.099.50.41710720.9420.1390.440.90993.5
2.09-2.149.30.33410950.9530.1120.3540.92595.5
2.14-2.199.30.27510960.9660.0930.2921.04595
2.19-2.259.30.23711030.9770.080.2511.09394.4
2.25-2.329.20.21110810.9810.0720.2231.21894.4
2.32-2.3990.18911190.9850.0640.21.17995.2
2.39-2.489.10.1610840.9880.0540.171.26994.3
2.48-2.588.90.14211130.9910.0480.151.33394.5
2.58-2.78.80.11811170.9930.040.1251.50194.6
2.7-2.848.60.10110980.9950.0350.1071.64595.7
2.84-3.028.40.08411260.9960.0290.091.88195.2
3.02-3.258.30.07111170.9970.0250.0762.04394.1
3.25-3.587.90.05511290.9980.020.0592.19495.5
3.58-4.0980.04711340.9980.0170.052.30296.2
4.09-5.168.60.04211920.9990.0140.0442.19598.3
5.16-5010.10.04112420.9990.0130.0432.16796.1

-
Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
REFMAC5.8.0073refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBO

3kbo


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.1611 / FOM work R set: 0.8571 / SU B: 6.843 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1489 / SU Rfree: 0.1395 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1098 4.9 %RANDOM
Rwork0.1632 21164 --
obs0.1655 22262 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.97 Å2 / Biso mean: 39.663 Å2 / Biso min: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å20 Å2
2---1.24 Å2-0 Å2
3---2.06 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 173 2443
Biso mean---46.46 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192335
X-RAY DIFFRACTIONr_bond_other_d0.0010.022264
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9623186
X-RAY DIFFRACTIONr_angle_other_deg0.83735177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12722.44998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4211522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_mcbond_it1.5182.131204
X-RAY DIFFRACTIONr_mcbond_other1.5182.1281203
X-RAY DIFFRACTIONr_mcangle_it2.1543.1831502
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 70 -
Rwork0.219 1550 -
all-1620 -
obs--94.46 %
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)
16.19683.65090.69135.3818-0.30525.33790.0635-0.03880.1806-0.0573-0.04050.42340.0303-0.586-0.0230.12370.01220.01810.1851-0.02610.0772-22.032-8.934-14.837
21.98121.3352-0.52966.06290.6117.31430.0613-0.16980.00710.5111-0.11870.1579-0.1245-0.25130.05730.18-0.01560.01720.1556-0.02740.0097-16.876-6.56-5.203
30.4051-0.22692.17878.4713-2.225512.31770.02780.1181-0.08160.7120.2056-1.1290.38150.8439-0.23350.34090.095-0.04930.3145-0.01910.2616-10-15.549-6.537
40.35910.5816-0.13452.3514-1.96443.8156-0.0096-0.04390.12060.02240.0760.04230.0528-0.1119-0.06640.1017-0.0006-0.01610.16080.00580.11973.101-6.338-39.069
52.6017-0.2467-0.15352.1217-0.34693.1029-0.0431-0.0848-0.121-0.08070.0198-0.00030.08860.01350.02330.12220.0339-0.0070.1450.0060.100210.905-19.864-32.308
63.0384-0.7960.65452.1566-0.01381.0332-0.1784-0.43590.34710.27560.1631-0.1816-0.0079-0.02190.01530.10610.0444-0.04360.1629-0.04950.053213.983-9.659-23.032
72.6904-1.2883-0.72933.47550.5051.6292-0.0975-0.07550.19670.18770.0718-0.0414-0.153-0.15780.02570.14370.0284-0.03290.141-0.00820.11221.570.069-25.284
83.5131-1.48870.45146.4896-1.95616.5260.0227-0.0375-0.45920.27120.02180.19640.9715-0.1446-0.04450.3003-0.07230.01080.0904-0.04460.0914-18.044-21.298-13.057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 37
2X-RAY DIFFRACTION2A38 - 75
3X-RAY DIFFRACTION3A76 - 98
4X-RAY DIFFRACTION4A99 - 135
5X-RAY DIFFRACTION5A136 - 180
6X-RAY DIFFRACTION6A181 - 253
7X-RAY DIFFRACTION7A254 - 285
8X-RAY DIFFRACTION8A286 - 313

+
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