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- PDB-2hq1: Crystal Structure of ORF 1438 a putative Glucose/ribitol dehydrog... -

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Basic information

Entry
Database: PDB / ID: 2hq1
TitleCrystal Structure of ORF 1438 a putative Glucose/ribitol dehydrogenase from Clostridium thermocellum
ComponentsGlucose/ribitol dehydrogenase
KeywordsOXIDOREDUCTASE / Glucose/ribitol dehydrogenase / CTH-1438 / STRUCTURAL GENOMICS / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / PSI / Protein Structure Initiative
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / steroid metabolic process / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / 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
3-oxoacyl-[acyl-carrier-protein] reductase / :
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacemet / Resolution: 1.9 Å
AuthorsSoutheast Collaboratory for Structural Genomics (SECSG) / Li, Y. / Shaw, N. / Xu, H. / Cheng, C. / Chen, L. / Liu, Z.J. / Rose, J.P. / Wang, B.C.
CitationJournal: To be Published
Title: Crystal Structure of ORF 1438 a putative Glucose/ ribitol dehydrogenase from Clostridium thermocellum
Authors: Li, Y. / Shaw, N. / Xu, H. / Cheng, C. / Chen, L. / Liu, Z.J. / ROSE, J.P. / WANG, B.C. / Southeast Collaboratory for Structural Genomics
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose/ribitol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)26,1061
Polymers26,1061
Non-polymers00
Water97354
1
A: Glucose/ribitol dehydrogenase

A: Glucose/ribitol dehydrogenase

A: Glucose/ribitol dehydrogenase

A: Glucose/ribitol dehydrogenase


Theoretical massNumber of molelcules
Total (without water)104,4254
Polymers104,4254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)77.982, 99.487, 69.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-270-

HOH

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Components

#1: Protein Glucose/ribitol dehydrogenase


Mass: 26106.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q4CFD1, UniProt: A3DDY9*PLUS, 17beta-estradiol 17-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growDetails: HANGING DROP VAPOR DIFUSION USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (9 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.1M AMMONIUM DIHYDROGEN PHOSPHATE AND 20% ...Details: HANGING DROP VAPOR DIFUSION USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (9 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 0.1M AMMONIUM DIHYDROGEN PHOSPHATE AND 20% W/V PEG 3350, SETUP AT 291K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2006 / Details: Rosenbaum
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9791
ReflectionResolution: 1.9→20 Å / Num. all: 20685 / Num. obs: 19128 / % possible obs: 92.68 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rsym value: 0.053 / Net I/σ(I): 21.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.23 / Num. unique all: 1282 / Rsym value: 0.352 / % possible all: 57.9

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Processing

Software
NameVersionClassification
CCP4model building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: Molecular Replacemet
Starting model: PDB entry 1EDO

1edo


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.103 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24902 1045 5.2 %RANDOM
Rwork0.23235 ---
all0.23321 19128 --
obs0.23321 19128 92.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.136 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--1.9 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 0 54 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221566
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9622128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9265223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.90926.73946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36315249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.654152
X-RAY DIFFRACTIONr_chiral_restr0.0660.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.2668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21104
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5421.51132
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93521727
X-RAY DIFFRACTIONr_scbond_it1.3333499
X-RAY DIFFRACTIONr_scangle_it2.0354.5398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 53 -
Rwork0.312 927 -
obs--61.95 %

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