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- PDB-4hng: The crystal structure of a short-chain dehydrogenases/reductase (... -

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Basic information

Entry
Database: PDB / ID: 4hng
TitleThe crystal structure of a short-chain dehydrogenases/reductase (wide type) from Veillonella parvula DSM 2008
ComponentsNAD-dependent epimerase/dehydratase
KeywordsISOMERASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


NAD(P)H-binding / NAD(P)-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
FORMIC ACID / NAD-dependent epimerase/dehydratase
Similarity search - Component
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a short-chain dehydrogenases/reductase (wide type) from Veillonella parvula DSM 2008
Authors: Tan, K. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.
History
DepositionOct 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Data collection
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1698
Polymers24,6841
Non-polymers4857
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.044, 61.839, 69.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. IT IS PREDICTED TO BE MONOMERIC.

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Components

#1: Protein NAD-dependent epimerase/dehydratase


Mass: 24683.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_0111 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1BQI7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Acetate, 0.1M Bis-Tris:HCl, 25% (w/v) PEG3350, 10mM NADP, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2012 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.5→24.5 Å / Num. all: 36592 / Num. obs: 36592 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 24.18 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 43.9
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1821 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 3R14

3r14
PDB Unreleased entry


Resolution: 1.5→24.378 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 20.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2023 1826 5 %random
Rwork0.1808 ---
obs0.1819 36529 99.63 %-
all-36529 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.616 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4453 Å2-0 Å2-0 Å2
2---5.5318 Å20 Å2
3---5.0865 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 29 202 1939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061795
X-RAY DIFFRACTIONf_angle_d0.9722436
X-RAY DIFFRACTIONf_dihedral_angle_d12.352673
X-RAY DIFFRACTIONf_chiral_restr0.066276
X-RAY DIFFRACTIONf_plane_restr0.004313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5005-1.54110.2721320.2582581X-RAY DIFFRACTION99
1.5411-1.58640.25381370.23792673X-RAY DIFFRACTION100
1.5864-1.63760.23471230.2092638X-RAY DIFFRACTION100
1.6376-1.69610.22351380.20782654X-RAY DIFFRACTION100
1.6961-1.7640.28521190.20012649X-RAY DIFFRACTION100
1.764-1.84430.2141520.1872651X-RAY DIFFRACTION100
1.8443-1.94140.20081360.17932676X-RAY DIFFRACTION100
1.9414-2.0630.21381440.19072656X-RAY DIFFRACTION100
2.063-2.22220.19791620.18142644X-RAY DIFFRACTION100
2.2222-2.44570.19751590.17792660X-RAY DIFFRACTION100
2.4457-2.79910.21381430.18662714X-RAY DIFFRACTION100
2.7991-3.52490.21921510.17612711X-RAY DIFFRACTION100
3.5249-24.38150.17021300.16872796X-RAY DIFFRACTION97
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)
18.92032.0092-0.3944.51642.29137.7721-0.05720.2240.7058-0.13970.3689-0.2658-0.77150.4354-0.23230.2086-0.04150.05050.2374-0.04870.2045-4.562614.5944-19.1686
23.9236-0.7566-0.16325.4835-2.19647.64890.0130.6593-0.1682-0.1452-0.00210.3964-0.2014-0.0031-0.01260.2104-0.01820.03820.3028-0.07070.2035-10.97838.5736-25.1167
33.6987-0.70481.34152.30571.69292.19570.39010.9938-0.4327-0.62870.1373-0.25010.75681.3924-0.42520.48250.0753-0.02360.3508-0.16010.2281-1.49115.3595-23.4213
43.5640.52060.32023.16681.58988.38910.04640.4821-0.3227-0.22450.5694-0.68460.32911.4948-0.53880.2669-0.00840.05180.4459-0.18480.34673.68887.8898-17.3672
54.855-0.3909-0.07944.515-1.33876.2444-0.22510.1644-0.1418-0.30480.2115-0.3560.01970.41660.05110.1747-0.00820.01380.1778-0.07040.1523-5.069911.7858-12.1168
67.54095.7345-5.25634.5445-4.75347.0973-0.0355-0.5177-0.210.31420.0164-0.62720.08450.78560.01210.17720.059-0.03910.3184-0.07550.2567-0.250310.5059-3.4835
78.25322.9151-1.44283.2124-0.53962.0603-0.0348-0.41050.09450.1209-0.04350.0045-0.020.12110.08010.1520.0043-0.01560.1758-0.03990.1109-13.820411.827-6.6315
86.7324-5.0350.43145.72081.39723.7886-0.1996-1.3354-0.90631.1210.2420.21620.7505-0.1862-0.00210.3118-0.08590.04970.21940.01920.375-26.6857-3.5399-3.4091
93.43121.56690.52833.84830.78052.1158-0.0036-0.2498-0.17610.2711-0.0052-0.11180.11120.08660.03720.14260.03580.01470.1723-0.0150.1449-14.53337.8674-4.1262
104.09490.7585-1.34433.88990.10331.5762-0.14030.2879-0.0104-0.3934-0.03830.23030.0543-0.19170.180.19670.0034-0.03950.23-0.02560.1697-23.40919.9048-17.1732
113.78761.40330.24944.58240.89642.5399-0.02440.09330.1357-0.2427-0.12880.1994-0.0511-0.21140.1330.17280.0502-0.02310.2002-0.03150.1745-23.127612.7157-12.6112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:12)
2X-RAY DIFFRACTION2chain 'A' and (resseq 13:25)
3X-RAY DIFFRACTION3chain 'A' and (resseq 26:46)
4X-RAY DIFFRACTION4chain 'A' and (resseq 47:68)
5X-RAY DIFFRACTION5chain 'A' and (resseq 69:81)
6X-RAY DIFFRACTION6chain 'A' and (resseq 82:94)
7X-RAY DIFFRACTION7chain 'A' and (resseq 95:113)
8X-RAY DIFFRACTION8chain 'A' and (resseq 114:125)
9X-RAY DIFFRACTION9chain 'A' and (resseq 126:155)
10X-RAY DIFFRACTION10chain 'A' and (resseq 156:190)
11X-RAY DIFFRACTION11chain 'A' and (resseq 191:217)

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