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- PDB-1nfr: Rv2002 gene product from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1nfr
TitleRv2002 gene product from Mycobacterium tuberculosis
ComponentsPutative oxidoreductase Rv2002
KeywordsOXIDOREDUCTASE / Directed evolution / GFP / SDR / hydroxysteroid dehydrogenase / structural genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / steroid catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / steroid metabolic process / plasma membrane
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase / 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYang, J.K. / Park, M.S. / Waldo, G.S. / Suh, S.W. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis
Authors: Yang, J.K. / Park, M.S. / Waldo, G.S. / Suh, S.W.
History
DepositionDec 16, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative oxidoreductase Rv2002
B: Putative oxidoreductase Rv2002
C: Putative oxidoreductase Rv2002
D: Putative oxidoreductase Rv2002
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9998
Polymers109,3454
Non-polymers2,6544
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19790 Å2
ΔGint-128 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.020, 120.020, 140.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein
Putative oxidoreductase Rv2002 / Rv2002 gene product


Mass: 27336.203 Da / Num. of mol.: 4 / Mutation: I6T, V47(MSE), T69K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: P69167, UniProt: P9WGT1*PLUS, 3alpha(or 20beta)-hydroxysteroid dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG 400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 Mammonium sulfate1reservoir
25.0 %(v/v)PEG4001reservoir
3100 mMsodium HEPES1reservoirpH7.5
414.4 mg/mlprotein1drop
520 mMTris-HCl1droppH8.0
60.1 mMPMSF1drop
72 mMNAD+1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 57609 / Num. obs: 57609 / % possible obs: 99.9 % / Biso Wilson estimate: 17.6 Å2
Reflection shellResolution: 2.1→2.2 Å / % possible all: 100
Reflection
*PLUS
Num. measured all: 288652 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3005896.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5866 10.2 %RANDOM
Rwork0.203 ---
all0.203 ---
obs0.203 57605 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7316 Å2 / ksol: 0.414345 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2--1.96 Å20 Å2
3----3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7120 0 176 385 7681
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it0.251.5
X-RAY DIFFRACTIONc_mcangle_it0.462
X-RAY DIFFRACTIONc_scbond_it0.252
X-RAY DIFFRACTIONc_scangle_it0.392.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 949 9.9 %
Rwork0.222 8594 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.ADD.PARAMPROTEIN.ADD.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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