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- PDB-5h5x: Crystal structure of NADH bound carbonyl reductase from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 5h5x
TitleCrystal structure of NADH bound carbonyl reductase from Streptomyces coelicolor
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / Carbonyl reductase / SDR family / COBE reductase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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
ISOPROPYL ALCOHOL / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Putative oxidoreductase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKong, X.-D. / Xu, J.-H. / Zhou, J.
CitationJournal: To Be Published
Title: Crystal structure of NADH bound carbonyl reductase from Streptomyces coelicolor
Authors: Li, M. / Kong, X.-D. / Zhou, J. / Yu, H.-L. / Zhang, Z.-J. / Xu, J.-H.
History
DepositionNov 10, 2016Deposition site: PDBJ / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
E: Putative oxidoreductase
F: Putative oxidoreductase
G: Putative oxidoreductase
H: Putative oxidoreductase
I: Putative oxidoreductase
J: Putative oxidoreductase
K: Putative oxidoreductase
L: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,50252
Polymers317,04812
Non-polymers9,45340
Water17,493971
1
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,81417
Polymers105,6834
Non-polymers3,13113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19640 Å2
ΔGint-92 kcal/mol
Surface area30550 Å2
MethodPISA
2
E: Putative oxidoreductase
F: Putative oxidoreductase
G: Putative oxidoreductase
H: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,87418
Polymers105,6834
Non-polymers3,19114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19880 Å2
ΔGint-87 kcal/mol
Surface area30410 Å2
MethodPISA
3
I: Putative oxidoreductase
J: Putative oxidoreductase
K: Putative oxidoreductase
L: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,81417
Polymers105,6834
Non-polymers3,13113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19440 Å2
ΔGint-91 kcal/mol
Surface area30090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.787, 187.787, 80.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Putative oxidoreductase


Mass: 26420.691 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Gene: SCO7363 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KYM4
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical...
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 8000, 0.1 M cacodylate sodium pH 6.5, 0.2 M Mg(OAc)2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 118981 / % possible obs: 84 % / Redundancy: 2.1 % / Biso Wilson estimate: 41.94 Å2 / Rmerge(I) obs: 0.141 / Net I/av σ(I): 4.008 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.382.20.632183.7
2.38-2.482.20.504183.9
2.48-2.592.10.421184.3
2.59-2.732.10.343183.6
2.73-2.920.272183.8
2.9-3.1220.217183.6
3.12-3.441.80.181182.8
3.44-3.931.80.151180.3
3.93-4.9520.117182.3
4.95-502.90.07191.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.496 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.42
RfactorNum. reflection% reflection
Rfree0.2426 5977 5.03 %
Rwork0.1792 --
obs0.1825 118935 83.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.52 Å2 / Biso mean: 35.5 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 2.3→32.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21403 0 622 971 22996
Biso mean--38.64 35.39 -
Num. residues----3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822406
X-RAY DIFFRACTIONf_angle_d1.23430531
X-RAY DIFFRACTIONf_chiral_restr0.0723524
X-RAY DIFFRACTIONf_plane_restr0.0053994
X-RAY DIFFRACTIONf_dihedral_angle_d16.2477739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2999-2.3260.33521920.25713738393083
2.326-2.35340.32871860.24763784397084
2.3534-2.38210.31691940.24593804399884
2.3821-2.41220.33932290.23233690391984
2.4122-2.4440.29131870.22493809399684
2.444-2.47740.31521950.22153736393184
2.4774-2.51280.2991790.21823771395084
2.5128-2.55030.29141890.21063835402484
2.5503-2.59010.2952060.21033731393784
2.5901-2.63260.30672060.2153763396984
2.6326-2.67790.32122130.21873726393984
2.6779-2.72660.28951940.2153775396984
2.7266-2.7790.28611500.21423824397484
2.779-2.83570.29042170.20683683390083
2.8357-2.89740.28152080.20693761396984
2.8974-2.96470.25821900.20423737392783
2.9647-3.03880.30711910.21533739393084
3.0388-3.12090.27081930.21953799399284
3.1209-3.21260.30141950.20513730392584
3.2126-3.31620.23551950.19843709390483
3.3162-3.43460.26752130.19743659387282
3.4346-3.5720.24161840.18533656384081
3.572-3.73430.23331940.17293587378180
3.7343-3.93090.23792050.17743594379980
3.9309-4.17670.24461960.16183612380881
4.1767-4.49850.16962030.14123579378280
4.4985-4.94970.1912150.13163815403086
4.9497-5.66270.19932270.13574306453396
5.6627-7.1220.18862300.144392462298
7.122-32.49950.1922010.14853614381581

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