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- PDB-3o0k: Crystal structure of ALDO/KETO reductase from brucella melitensis -

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Basic information

Entry
Database: PDB / ID: 3o0k
TitleCrystal structure of ALDO/KETO reductase from brucella melitensis
ComponentsAldo/keto reductase
KeywordsOXIDOREDUCTASE / SSGCID / ALS COLLABORATIVE CRYSTALLOGRAPHY / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


2,5-didehydrogluconate reductase activity / : / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
Aldo-keto reductase family 5C2 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 5C2 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrucella melitensis biovar (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of ALDO/KETO reductase from brucella melitensis
Authors: SSGCID / Abendroth, J. / Edwards, T.E. / Staker, B.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 6, 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: Aldo/keto reductase
B: Aldo/keto reductase
C: Aldo/keto reductase
D: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,46412
Polymers126,8484
Non-polymers6178
Water13,529751
1
A: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8663
Polymers31,7121
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8663
Polymers31,7121
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8663
Polymers31,7121
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Aldo/keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8663
Polymers31,7121
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.180, 50.860, 115.350
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldo/keto reductase


Mass: 31711.936 Da / Num. of mol.: 4 / Fragment: UNP residues 19-279
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar (bacteria) / Strain: ABORTUS 2308 / Gene: 3827820, BAB2_0177 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YII2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 1.87 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: EBS JCSG+ SCREEN, D9: 0.17M AMMONIUM SULPHATE, 25.5% PEG 4000, 15% GLYCEROL; BRABA.00019.A AT 73MG/ML, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 28, 2010 / Details: Rigaku/Osmic VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 87518 / Num. obs: 87040 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 23.54 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.65
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6314 / % possible all: 98.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1mzr, residues 1-220, modified with CCP4 program CHAINSAW

1mzr


Resolution: 1.8→46.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.92 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4353 5 %RANDOM
Rwork0.179 ---
all0.182 87518 --
obs0.182 86857 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.4 Å2
2---0.49 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8049 0 40 751 8840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228341
X-RAY DIFFRACTIONr_bond_other_d0.0010.025514
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.94511344
X-RAY DIFFRACTIONr_angle_other_deg0.938313517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37951046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88924.827375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6491534
X-RAY DIFFRACTIONr_chiral_restr0.0950.21285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021629
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.781.55150
X-RAY DIFFRACTIONr_mcbond_other0.2311.52103
X-RAY DIFFRACTIONr_mcangle_it1.33228314
X-RAY DIFFRACTIONr_scbond_it2.17733191
X-RAY DIFFRACTIONr_scangle_it3.4194.53018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 334 -
Rwork0.252 5959 -
obs--98.84 %
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)
10.8508-0.02970.50450.8331-0.18050.657-0.00490.05470.0111-0.03330.001-0.00680.01490.00230.00390.0459-0.00080.02930.0614-0.00440.02025.57910.90699.835
20.8822-0.01130.29090.70930.11140.34960.0278-0.0632-0.009-0.0211-0.0124-0.0267-0.031-0.0036-0.01540.029-0.01030.02740.03180.00980.0422-19.88711.47972.299
30.60980.0669-0.09210.7790.08960.3089-0.00810.03810.0081-0.05920.0216-0.04530.0042-0.0084-0.01350.0130.0020.02560.02390.01320.0688-29.3113.23446.463
40.7606-0.10880.14570.8594-0.2410.6066-0.0309-0.04210.02330.03980.0283-0.0358-0.01090.03880.00260.02230.00240.01950.0319-0.01690.033915.61713.588126.081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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