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- PDB-3gz4: Crystal structure of putative short chain dehydrogenase FROM ESCH... -

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Basic information

Entry
Database: PDB / ID: 3gz4
TitleCrystal structure of putative short chain dehydrogenase FROM ESCHERICHIA COLI CFT073 complexed with NADPH
ComponentsHypothetical oxidoreductase yciK
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / dehydrogenase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / short chain dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
Chem-NDP / Hypothetical oxidoreductase yciK / Hypothetical oxidoreductase yciK
Similarity search - Component
Biological speciesEscherichia coli O6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMalashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative short chain dehydrogenase FROM ESCHERICHIA COLI CFT073 complexed with NADPH
Authors: Malashkevich, V.N. / Toro, R. / Morano, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 24, 2012Group: Structure summary
Revision 1.3Dec 4, 2013Group: Non-polymer description
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Hypothetical oxidoreductase yciK
B: Hypothetical oxidoreductase yciK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8474
Polymers58,3562
Non-polymers1,4912
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-25 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.794, 130.511, 47.934
Angle α, β, γ (deg.)90.000, 115.060, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-99999 - 99999
2111B-99999 - 99999

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Components

#1: Protein Hypothetical oxidoreductase yciK


Mass: 29178.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6 (bacteria) / Strain: CFT073 / Gene: AAN80202.1, c1736, yciK / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q8FHV3, UniProt: A0A0H2V6Y9*PLUS, Oxidoreductases
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1 M Na-cacodylate, 0.2 M magnesium acetate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.946
11-H, -K, H+L20.054
ReflectionResolution: 2→50 Å / Num. obs: 21681 / % possible obs: 65.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.143 / Χ2: 1.117 / Net I/σ(I): 5.019
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.031.20.8772241.599114.1
2.03-2.071.10.5923471.472120.7
2.07-2.111.20.6844821.43129.3
2.11-2.151.20.626621.261140
2.15-2.21.20.5156890.973142.3
2.2-2.251.20.4898611.517152.3
2.25-2.311.30.6038741.164153.1
2.31-2.371.30.4310030.923161
2.37-2.441.40.41210510.956163.2
2.44-2.521.40.35811101.24168.1
2.52-2.611.50.40812051.181172.8
2.61-2.711.60.37113140.989179.2
2.71-2.841.80.35314121.143186.1
2.84-2.9920.32515310.989192
2.99-3.172.20.28215301.081193.4
3.17-3.422.30.19515421.153192.1
3.42-3.762.40.14415031.209191.4
3.76-4.312.40.10615081.142190.7
4.31-5.432.40.09214711.049188
5.43-502.50.0813621.139180.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.88 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.15 Å
Translation2.5 Å36.15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.803 / SU B: 14.77 / SU ML: 0.161 / SU R Cruickshank DPI: 0.116 / SU Rfree: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1026 5 %RANDOM
Rwork0.226 ---
obs0.227 20664 72.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 75.26 Å2 / Biso mean: 35.794 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å20 Å210 Å2
2---4.04 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 96 116 3941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223920
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9935337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60124.246179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66215654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7871533
X-RAY DIFFRACTIONr_chiral_restr0.0940.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212959
X-RAY DIFFRACTIONr_mcbond_it0.8993.52404
X-RAY DIFFRACTIONr_mcangle_it3.974503859
X-RAY DIFFRACTIONr_scbond_it9.461501516
X-RAY DIFFRACTIONr_scangle_it0.8454.51477
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1888 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.315
TIGHT THERMAL3.0310
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 43 -
Rwork0.454 760 -
all-803 -
obs--38.49 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
112.07110.815414.8002
24.4822-27.9873-1.6833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 243
2X-RAY DIFFRACTION1A500
3X-RAY DIFFRACTION1A259 - 374
4X-RAY DIFFRACTION2B3 - 242
5X-RAY DIFFRACTION2B500

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