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

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Basic information

Entry
Database: PDB / ID: 4hnh
TitleThe crystal structure of a short-chain dehydrogenases/reductase (wide type) from Veillonella parvula DSM 2008 in complex with NADP
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TRIETHYLAMMONIUM ION / NAD-dependent epimerase/dehydratase
Similarity search - Component
Biological speciesVeillonella parvula (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 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 in complex with NADP.
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
B: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,44213
Polymers49,3682
Non-polymers2,07411
Water7,999444
1
A: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8318
Polymers24,6841
Non-polymers1,1477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6115
Polymers24,6841
Non-polymers9274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.219, 71.687, 65.016
Angle α, β, γ (deg.)90.00, 121.44, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. IT IS PREDICTED TO BE MONOMERIC.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NAD-dependent epimerase/dehydratase


Mass: 24683.980 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 455 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-TEA / TRIETHYLAMMONIUM ION / Triethylamine


Mass: 102.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16N
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Sodium Chloride, 0.1M Bis-Tris:HCl, 25% (w/v) PEG3350, 10mM NADP, pH 5.5, 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
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.58→29 Å / Num. all: 57582 / Num. obs: 57582 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.4
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2635 / % possible all: 90.1

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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: 1.576→28.999 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 2916 5.06 %random
Rwork0.1749 ---
obs0.1763 57579 97.51 %-
all-57579 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.22 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4596 Å2-0 Å24.3211 Å2
2---2.6407 Å2-0 Å2
3---3.1003 Å2
Refinement stepCycle: LAST / Resolution: 1.576→28.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 132 444 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063790
X-RAY DIFFRACTIONf_angle_d1.0555195
X-RAY DIFFRACTIONf_dihedral_angle_d13.4151454
X-RAY DIFFRACTIONf_chiral_restr0.066593
X-RAY DIFFRACTIONf_plane_restr0.004657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.576-1.60190.35031120.32492110X-RAY DIFFRACTION80
1.6019-1.62950.36991450.31892543X-RAY DIFFRACTION95
1.6295-1.65910.32111450.29042553X-RAY DIFFRACTION97
1.6591-1.6910.30021400.27312590X-RAY DIFFRACTION98
1.691-1.72550.28331420.23642639X-RAY DIFFRACTION98
1.7255-1.76310.26431510.21862607X-RAY DIFFRACTION98
1.7631-1.80410.25511380.21222619X-RAY DIFFRACTION98
1.8041-1.84920.2421460.19982572X-RAY DIFFRACTION98
1.8492-1.89920.21781400.1762622X-RAY DIFFRACTION98
1.8992-1.9550.23621280.17872630X-RAY DIFFRACTION99
1.955-2.01810.23531460.16842647X-RAY DIFFRACTION99
2.0181-2.09020.20011340.16872651X-RAY DIFFRACTION99
2.0902-2.17390.21821330.16952644X-RAY DIFFRACTION99
2.1739-2.27280.20691480.16082620X-RAY DIFFRACTION99
2.2728-2.39260.16941290.16412683X-RAY DIFFRACTION99
2.3926-2.54240.22131300.16662652X-RAY DIFFRACTION100
2.5424-2.73860.23811390.17342665X-RAY DIFFRACTION99
2.7386-3.01390.18991540.17372662X-RAY DIFFRACTION100
3.0139-3.44940.18121430.15912682X-RAY DIFFRACTION99
3.4494-4.34350.14421560.14072632X-RAY DIFFRACTION99
4.3435-29.00390.17351170.1682640X-RAY DIFFRACTION96
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)
11.27750.2333-0.1413.541-0.64810.83070.0164-0.1264-0.09790.1945-0.1035-0.29880.02410.14350.05620.10190.0027-0.01780.14140.02110.1061-13.8382-5.29961.0813
22.35090.5262-0.21330.7468-0.04180.84360.00510.01990.025-0.0037-0.01030.01070.0076-0.04140.0040.1114-0.0008-0.01420.09820.00640.077-27.30313.2475-10.144
33.6569-0.43790.80383.88930.09183.05940.0116-0.11220.13720.130.0515-0.0104-0.1112-0.0481-0.04780.0668-0.01840.02380.08270.00630.0702-5.14737.865-17.4962
42.9050.5232-0.37711.8383-0.22584.3760.0667-0.0325-0.0475-0.0426-0.0499-0.1316-0.25210.2412-0.0260.0912-0.02390.00480.09690.01110.11563.395835.3933-22.6144
52.36520.68340.69993.53832.28574.5818-0.0301-0.1579-0.2698-0.07850.0872-0.55590.10510.189-0.0120.0917-0.00670.02570.08390.03880.139-0.143723.2651-16.4866
64.54860.36-0.1521.93360.07031.19570.1211-0.1513-0.70050.14610.0552-0.22960.162-0.0861-0.19460.1463-0.0335-0.04450.09360.02250.1712-11.613522.7676-15.8883
71.74440.10090.02891.7067-0.27111.72690.00870.061-0.0571-0.15360.03830.21670.089-0.2058-0.0050.0866-0.0215-0.01290.08640.00370.0813-18.305625.4417-20.7376
81.72820.498-0.98122.97430.24970.6583-0.00510.21310.16130.11190.00320.4582-0.1660.0170.02570.1170.00880.0430.12560.01750.1817-21.03229.0457-15.1645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:94)
2X-RAY DIFFRACTION2chain 'A' and (resseq 95:218)
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:25)
4X-RAY DIFFRACTION4chain 'B' and (resseq 26:68)
5X-RAY DIFFRACTION5chain 'B' and (resseq 69:94)
6X-RAY DIFFRACTION6chain 'B' and (resseq 95:113)
7X-RAY DIFFRACTION7chain 'B' and (resseq 114:190)
8X-RAY DIFFRACTION8chain 'B' and (resseq 191:217)

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