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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5unn
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in apo form
ComponentsNADPH-dependent glyoxylate/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / New York Structural Genomics Research Consortium / NADP-dependent dehydrogenase / Sinorhizobium meliloti / PSI-Biology / NYSGRC
Function / homology
Function and homology information


NAD binding / oxidoreductase activity
Similarity search - Function
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
NAD-dependent dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShabalin, I.G. / LaRowe, C. / Kutner, J. / Gasiorowska, O.A. / Handing, K.B. / 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 / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6315
Polymers69,4112
Non-polymers2203
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-38 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.592, 128.592, 122.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11B-538-

HOH

21B-765-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 93 - 291 / Label seq-ID: 93 - 291

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein NADPH-dependent glyoxylate/hydroxypyruvate reductase


Mass: 34705.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc02828 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q92T34, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 3.66 Å3/Da / Density % sol: 66.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG suite I condition # 88 (0.1 M Sodium citrate ...Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG suite I condition # 88 (0.1 M Sodium citrate pH=5.6, 20% v/v 2-Propanol, 20% w/v PEG 4000 ) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci)

-
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: Apr 18, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 67353 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Rrim(I) all: 0.117 / Rsym value: 0.108 / Χ2: 1.3 / Net I/av σ(I): 18.5 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2-2.036.60.9021.70.6150.3890.9860.9020.852100
2.03-2.076.70.7870.6350.340.8610.877100
2.07-2.116.70.6760.7260.290.7380.923100
2.11-2.156.70.5570.7850.2380.6080.958100
2.15-2.26.70.4640.8550.1980.5070.991100
2.2-2.256.80.3940.880.1670.431.004100
2.25-2.316.80.3710.8930.1570.4041.025100
2.31-2.376.80.3320.9060.140.3611.059100
2.37-2.446.90.2750.9430.1150.2991.117100
2.44-2.526.90.2360.9550.0990.2571.143100
2.52-2.6170.2090.9660.0870.2271.205100
2.61-2.7170.1830.9760.0750.1981.256100
2.71-2.847.10.1490.9830.0610.1611.346100
2.84-2.997.10.120.990.0490.131.45100
2.99-3.177.10.1030.9920.0410.1111.631100
3.17-3.427.20.0850.9950.0340.0921.727100
3.42-3.767.20.070.9950.0280.0761.985100
3.76-4.317.20.0580.9970.0230.0631.893100
4.31-5.437.20.0490.9980.0190.0521.71499.9
5.43-506.90.0460.9980.0190.051.60999.8

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0P

4z0p


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.475 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The catalytic domain (residues 1-95 and 287-319) is highly disordered in this structure. Only fragments of the ...Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The catalytic domain (residues 1-95 and 287-319) is highly disordered in this structure. Only fragments of the catalytic are visible in the chain A. Chain B has the domain completely disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 3517 5.2 %RANDOM
Rwork0.1468 ---
obs0.1482 63691 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 262.72 Å2 / Biso mean: 44.268 Å2 / Biso min: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 13 659 4096
Biso mean--52.67 49.85 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193521
X-RAY DIFFRACTIONr_bond_other_d0.0020.023345
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9534772
X-RAY DIFFRACTIONr_angle_other_deg0.92737651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37223.103145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18115545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9161525
X-RAY DIFFRACTIONr_chiral_restr0.0830.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
Refine LS restraints NCS

Ens-ID: 1 / Number: 12188 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 251 -
Rwork0.239 4601 -
all-4852 -
obs--98.68 %
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)
18.4392-0.363.83281.3531.22284.9365-0.11171.8788-0.896-0.32340.296-0.1945-0.06190.9653-0.18430.57480.02230.37870.6519-0.23860.372783.62319.94-0.663
20.2883-0.25560.19010.9241-0.56330.45580.05100.00270.08240.0051-0.03810.0035-0.0066-0.05620.252200.00480.23420.02430.34368.62230.54925.59
30.3815-0.2598-0.05271.1162-0.40970.5589-0.02280.03150.03730.0973-0.0369-0.03690.01140.02420.05960.2625-0.0102-0.02280.23230.02390.334472.34719.60533.433
41.78730.2779-0.93041.7592-0.03551.8513-0.02240.0896-0.0885-0.18060.05770.05340.2059-0.1779-0.03540.2739-0.0259-0.04380.23060.01170.308963.52615.37919.217
50.03890.05870.041.5665-0.50.28340.01770.0220.01540.02260.04520.05940.0025-0.0467-0.0630.24980.00910.01970.24640.02010.35465.72138.27416.772
60.2854-0.1930.00730.7243-0.34810.4262-0.0121-0.0073-0.0238-0.03430.06530.115-0.0056-0.0719-0.05320.23010.00810.01020.2590.03530.349557.45246.68111.227
793.2827-28.81464.429149.6934-42.530357.08431.8520.92130.48353.0983-2.8482-1.3447-0.7112.00360.99620.9475-0.34060.18290.9351-0.11030.217356.08947.5740.888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 74
2X-RAY DIFFRACTION1A288 - 313
3X-RAY DIFFRACTION2A91 - 170
4X-RAY DIFFRACTION3A171 - 261
5X-RAY DIFFRACTION4A262 - 287
6X-RAY DIFFRACTION5B93 - 170
7X-RAY DIFFRACTION6B171 - 287
8X-RAY DIFFRACTION7B288 - 292

+
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