[English] 日本語
Yorodumi
- PDB-5uog: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uog
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in apo form
ComponentsNADPH-dependent glyoxylate/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / NADPH-dependent glyoxylate/hydroxypyruvate reductase / NADP / NYSGRC / Sinorhizobium meliloti / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / metal ion binding / cytosol
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShabalin, I.G. / Handing, K.B. / Gasiorowska, O.A. / Cooper, D.R. / 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/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Authors: Kutner, J. / Shabalin, I.G. / Matelska, D. / Handing, K.B. / Gasiorowska, O. / Sroka, P. / Gorna, M.W. / Ginalski, K. / Wozniak, K. / Minor, W.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 16, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_ec / _struct.pdbx_descriptor
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH-dependent glyoxylate/hydroxypyruvate reductase
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8019
Polymers147,3214
Non-polymers4805
Water17,511972
1
A: NADPH-dependent glyoxylate/hydroxypyruvate reductase
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9485
Polymers73,6602
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-66 kcal/mol
Surface area25790 Å2
MethodPISA
2
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8524
Polymers73,6602
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-52 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.583, 176.583, 135.008
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGALAALAAA3 - 31925 - 341
21ARGARGALAALABB3 - 31925 - 341
12ARGARGALAALAAA3 - 31925 - 341
22ARGARGALAALACC3 - 31925 - 341
13ARGARGARGARGAA3 - 31825 - 340
23ARGARGARGARGDD3 - 31825 - 340
14ARGARGALAALABB3 - 31925 - 341
24ARGARGALAALACC3 - 31925 - 341
15SERSERARGARGBB2 - 31824 - 340
25SERSERARGARGDD2 - 31824 - 340
16ARGARGARGARGCC3 - 31825 - 340
26ARGARGARGARGDD3 - 31825 - 340

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
NADPH-dependent glyoxylate/hydroxypyruvate reductase


Mass: 36830.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc04462 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92LZ4, hydroxypyruvate reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 5 mM NADPH were mixed with 0.2 ul of the MCSG Suite 3 condition #61 (0.1 M ...Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 5 mM NADPH were mixed with 0.2 ul of the MCSG Suite 3 condition #61 (0.1 M Citric acid pH=3.5, 2 M Ammonium sulfate) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). The protein was crystallized with the His-tag

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2014
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.505
11K, H, -L20.495
ReflectionResolution: 2.4→50 Å / Num. obs: 61899 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.04 / Rrim(I) all: 0.073 / Rsym value: 0.061 / Χ2: 1.117 / Net I/av σ(I): 22.7 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2.4-2.443.20.63231130.6850.4220.7610.630.794100
2.44-2.493.20.5510.6950.370.6660.861100
2.49-2.533.20.4670.7740.3130.5640.839100
2.53-2.593.20.4180.7950.2810.5050.86100
2.59-2.643.20.3640.8370.2440.4390.83100
2.64-2.73.20.3080.8910.2060.3710.876100
2.7-2.773.20.2440.9230.1630.2940.897100
2.77-2.853.20.2030.9480.1360.2450.886100
2.85-2.933.20.1650.9620.110.1990.938100
2.93-3.023.20.1380.9770.0920.1660.934100
3.02-3.133.20.1110.9830.0740.1340.995100
3.13-3.263.20.0890.9870.0590.1071.05100
3.26-3.413.20.0750.9910.050.091.13100
3.41-3.583.20.0580.9950.0390.071.239100
3.58-3.813.20.0490.9950.0320.0591.391100
3.81-4.13.20.0470.9580.0320.0571.712100
4.1-4.523.20.040.9970.0260.0481.669100
4.52-5.173.10.0370.9970.0240.0441.596100
5.17-6.513.10.0360.9970.0240.0431.291100
6.51-503.20.0350.9960.0230.0421.60699.3

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J23
Resolution: 2.4→36.78 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.249 / SU ML: 0.104 / SU R Cruickshank DPI: 0.0544 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.041
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 2939 4.8 %RANDOM
Rwork0.1355 ---
obs0.1381 58425 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130 Å2 / Biso mean: 57.536 Å2 / Biso min: 22.91 Å2
Baniso -1Baniso -2Baniso -3
1--12.97 Å2-0 Å2-0 Å2
2---12.97 Å2-0 Å2
3---25.94 Å2
Refinement stepCycle: final / Resolution: 2.4→36.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9325 0 25 972 10322
Biso mean--62.77 53.98 -
Num. residues----1271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199516
X-RAY DIFFRACTIONr_bond_other_d0.0050.029388
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.98313021
X-RAY DIFFRACTIONr_angle_other_deg1.132321434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53351265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68822.819337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.657151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0021580
X-RAY DIFFRACTIONr_chiral_restr0.0680.21611
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110761
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022027
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A384400.05
12B384400.05
21A385600.05
22C385600.05
31A377700.05
32D377700.05
41B379620.06
42C379620.06
51B379700.03
52D379700.03
61C375200.06
62D375200.06
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 204 -
Rwork0.156 4335 -
all-4539 -
obs--99.67 %
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)
12.97220.2506-0.89343.66220.00393.7250.01990.0750.0386-0.2943-0.0455-0.6429-0.22960.32920.02560.20750.00010.06560.264-0.00560.119868.33581.47580.632
22.6392-0.93392.33312.4534-1.24923.5704-0.00550.09370.230.05050.0729-0.3578-0.15230.2594-0.06740.1773-0.00230.0260.2266-0.04090.163170.45883.5687.352
32.272-0.2748-0.98862.075-0.04342.6899-0.0369-0.21410.0320.19040.145-0.13940.27240.1286-0.10820.2330.0302-0.00030.26130.00530.037761.48777.8793.219
40.5332-0.1710.07710.84340.09730.9456-0.0037-0.0183-0.01880.14570.03880.0780.0997-0.1297-0.03520.2368-0.01070.00410.2386-0.030.040861.31347.29386.276
50.5701-0.6003-0.34552.10730.7970.37180.0318-0.0850.01050.0543-0.00140.0062-0.0023-0.0265-0.03040.2384-0.00350.01680.2674-0.01410.040962.13769.42384.848
64.13412.2631.2435.51781.28686.1086-0.099-0.0149-0.1992-0.04290.1234-0.27450.0680.274-0.02440.23190.0238-0.06290.22730.00440.123863.7814.66368.282
78.0049-1.4707-0.80531.4664-4.16315.77910.432-0.24710.7687-0.1067-0.4101-0.21190.08041.898-0.02180.2677-0.04030.0560.6499-0.26130.340273.06514.88959.066
82.21830.01330.16293.29330.68323.3672-0.21380.24030.0142-0.27270.2583-0.1471-0.20160.3933-0.04460.2303-0.0751-0.05240.2551-0.0170.054661.60518.59455.223
90.3279-0.3705-0.06481.4213-0.47430.31710.15540.0905-0.0563-0.2947-0.10890.17050.052-0.0476-0.04660.24940.0073-0.07820.2798-0.04820.037158.78750.98466.097
100.07550.1550.13560.95060.64430.45940.0450.0256-0.0545-0.24150.0252-0.0645-0.10080.0033-0.07020.32430.0032-0.06720.2586-0.03540.045362.46337.8859.076
111.5659-0.65880.26351.46620.54891.3161-0.01760.055-0.17990.0367-0.04030.11880.0785-0.16680.05780.2326-0.01980.01360.21180.03010.0659-16.48333.12677.24
120.4736-0.65630.31380.9676-0.39060.59790.0577-0.01-0.03250.00570.08310.0063-0.02320.056-0.14080.2556-0.0153-0.05480.2443-0.01140.059612.2120.72584.583
131.3654-0.40510.64110.34340.46518.26570.08570.1010.3707-0.03950.0663-0.1481-0.58230.3635-0.15210.3193-0.05050.02250.25450.07660.239220.30832.52278.658
141.1753-0.02660.08680.4605-0.16341.40210.12010.15760.0946-0.1329-0.11120.0232-0.0740.0816-0.0090.2410.0131-0.01170.26120.00290.019514.55620.15371.949
151.9824-1.47972.08122.3729-2.08713.0683-0.13720.060.0960.19380.051-0.0812-0.23190.21110.08610.2577-0.0181-0.00030.22090.02040.0322-7.46941.28580.188
162.93411.04971.10463.5141-0.12910.50980.10270.1459-0.4284-0.17340.0471-0.24080.05810.0686-0.14990.2340.0013-0.01260.352-0.09250.0847.7716.19797.263
171.32230.50310.4111.02840.57011.05960.1901-0.3139-0.17880.1952-0.05-0.12310.1681-0.2386-0.140.1864-0.0455-0.06060.4113-0.03180.060241.0984.601108.171
180.5718-0.6391-0.19380.78910.15440.1374-0.1004-0.07240.06670.10830.1332-0.0727-0.025-0.0096-0.03270.2915-0.02-0.05610.2658-0.02250.074612.17622.21993.374
1913.51192.76121.98091.19341.6562.78580.02870.05760.54780.15540.2099-0.05090.3210.4272-0.23870.33680.0703-0.18420.3686-0.16050.284125.53734.775109.482
201.4216-0.57360.53370.3384-0.20640.2057-0.1496-0.2217-0.02660.15370.1654-0.0594-0.0715-0.0507-0.01570.30330.0279-0.07590.3147-0.06360.050923.13218.759105.812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 17
2X-RAY DIFFRACTION2A18 - 60
3X-RAY DIFFRACTION3A61 - 92
4X-RAY DIFFRACTION4A93 - 259
5X-RAY DIFFRACTION5A260 - 319
6X-RAY DIFFRACTION6B2 - 24
7X-RAY DIFFRACTION7B25 - 37
8X-RAY DIFFRACTION8B38 - 93
9X-RAY DIFFRACTION9B94 - 202
10X-RAY DIFFRACTION10B205 - 319
11X-RAY DIFFRACTION11C3 - 79
12X-RAY DIFFRACTION12C80 - 154
13X-RAY DIFFRACTION13C155 - 174
14X-RAY DIFFRACTION14C175 - 278
15X-RAY DIFFRACTION15C279 - 319
16X-RAY DIFFRACTION16D-5 - 23
17X-RAY DIFFRACTION17D24 - 93
18X-RAY DIFFRACTION18D94 - 167
19X-RAY DIFFRACTION19D168 - 177
20X-RAY DIFFRACTION20D178 - 319

+
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