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- PDB-3k1y: X-ray structure of oxidoreductase from corynebacterium diphtheria... -

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Basic information

Entry
Database: PDB / ID: 3k1y
TitleX-ray structure of oxidoreductase from corynebacterium diphtheriae. orthorombic crystal form, northeast structural genomics consortium target cdr100d
Componentsoxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / CdR100D / Q6NGS1
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Uncharacterised protein family, CE1759 / : / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKuzin, A. / Lew, S. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. ...Kuzin, A. / Lew, S. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target CdR100D
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: oxidoreductase
B: oxidoreductase
C: oxidoreductase
D: oxidoreductase
E: oxidoreductase
F: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,28022
Polymers122,7436
Non-polymers1,53716
Water3,693205
1
A: oxidoreductase
B: oxidoreductase
C: oxidoreductase
F: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,78914
Polymers81,8294
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-182 kcal/mol
Surface area27730 Å2
MethodPISA
2
D: oxidoreductase
E: oxidoreductase
hetero molecules

D: oxidoreductase
E: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,98116
Polymers81,8294
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10250 Å2
ΔGint-248 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.170, 141.379, 201.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-182-

SO4

21C-182-

SO4

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Components

#1: Protein
oxidoreductase


Mass: 20457.164 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DIP1437 / Plasmid: pET 14-15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q6NGS1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growpH: 4.6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 2.2M ammonium sulfate, 0.1M sodium acetate. 3% ethanol. pH 4.6. VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97879 0.91837 0.97926
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2009 / Details: Flat collimating mirror,
RadiationMonochromator: Double crystal monochromator Si(111). A second set of Si(220)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978791
20.918371
30.979261
ReflectionResolution: 2.5→30 Å / Num. obs: 43361 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 17.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_115refinement
PDB_EXTRACT3data extraction
DENZOdata reduction
SCALAdata scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.88 Å / SU ML: 0.34 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 4097 5 %
Rwork0.229 --
obs0.229 82977 99.8 %
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7950 0 80 205 8235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018128
X-RAY DIFFRACTIONf_angle_d1.33911059
X-RAY DIFFRACTIONf_dihedral_angle_d18.1892845
X-RAY DIFFRACTIONf_chiral_restr0.0841397
X-RAY DIFFRACTIONf_plane_restr0.0061382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4996-2.5540.33541300.27842487X-RAY DIFFRACTION98
2.554-2.61330.28961300.27492549X-RAY DIFFRACTION100
2.6133-2.67860.28271350.26732554X-RAY DIFFRACTION100
2.6786-2.7510.24951410.26432527X-RAY DIFFRACTION100
2.751-2.83190.23581360.24572546X-RAY DIFFRACTION100
2.8319-2.92320.2221220.24592567X-RAY DIFFRACTION100
2.9232-3.02760.22481180.24782571X-RAY DIFFRACTION100
3.0276-3.14870.26621300.23192580X-RAY DIFFRACTION100
3.1487-3.29190.24451530.23592542X-RAY DIFFRACTION100
3.2919-3.46520.24511330.24712587X-RAY DIFFRACTION100
3.4652-3.68190.23381340.22712559X-RAY DIFFRACTION100
3.6819-3.96560.23911540.20862584X-RAY DIFFRACTION100
3.9656-4.36360.19371340.18922579X-RAY DIFFRACTION100
4.3636-4.99250.18311270.17012598X-RAY DIFFRACTION100
4.9925-6.28030.25991560.21172622X-RAY DIFFRACTION100
6.2803-29.87820.20961470.20392717X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.896 Å / Origin y: 37.3419 Å / Origin z: -28.8453 Å
111213212223313233
T0.034 Å20.0171 Å20.0146 Å2-0.0454 Å20.0026 Å2--0.0202 Å2
L0.2118 °2-0.1015 °20.2326 °2-0.1759 °2-0.2108 °2--0.2343 °2
S-0.0022 Å °0.0265 Å °0.055 Å °-0.0041 Å °-0.0531 Å °-0.0497 Å °0.0406 Å °-0.0112 Å °-0.0059 Å °
Refinement TLS groupSelection details: all

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