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- PDB-4z26: Mimivirus R135 (residues 51-702) -

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Basic information

Entry
Database: PDB / ID: 4z26
TitleMimivirus R135 (residues 51-702)
ComponentsPutative GMC-type oxidoreductase R135
KeywordsOXIDOREDUCTASE / GMC oxidoreductase / FAD / fiber
Function / homology
Function and homology information


choline dehydrogenase activity / glycine betaine biosynthetic process from choline / Oxidoreductases / host cell membrane / virion component / flavin adenine dinucleotide binding / identical protein binding / membrane
Similarity search - Function
GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Putative GMC-type oxidoreductase R135
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.915 Å
AuthorsKlose, T. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Structure / Year: 2015
Title: A Mimivirus Enzyme that Participates in Viral Entry.
Authors: Klose, T. / Herbst, D.A. / Zhu, H. / Max, J.P. / Kenttamaa, H.I. / Rossmann, M.G.
History
DepositionMar 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references / Refinement description / Structure summary
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Jun 17, 2015Group: Database references
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Putative GMC-type oxidoreductase R135
B: Putative GMC-type oxidoreductase R135
C: Putative GMC-type oxidoreductase R135
D: Putative GMC-type oxidoreductase R135
E: Putative GMC-type oxidoreductase R135
F: Putative GMC-type oxidoreductase R135
G: Putative GMC-type oxidoreductase R135
H: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)577,12816
Polymers570,8438
Non-polymers6,2848
Water12,592699
1
A: Putative GMC-type oxidoreductase R135
B: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-32 kcal/mol
Surface area43520 Å2
MethodPISA
2
C: Putative GMC-type oxidoreductase R135
hetero molecules

D: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area7860 Å2
ΔGint-33 kcal/mol
Surface area43440 Å2
MethodPISA
3
E: Putative GMC-type oxidoreductase R135
H: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-29 kcal/mol
Surface area43720 Å2
MethodPISA
4
F: Putative GMC-type oxidoreductase R135
hetero molecules

G: Putative GMC-type oxidoreductase R135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,2824
Polymers142,7112
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7850 Å2
ΔGint-34 kcal/mol
Surface area43370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.318, 240.503, 295.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative GMC-type oxidoreductase R135


Mass: 71355.430 Da / Num. of mol.: 8 / Fragment: UNP residues 51-702
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R135 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UPL2, Oxidoreductases
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, ammonium formate, 1-n-Butyl-3-methylimidazolium n-octylsulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.91→29.909 Å / Num. obs: 158141 / % possible obs: 96.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.182 / Net I/σ(I): 8.4
Reflection shellResolution: 2.91→2.99 Å / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.3 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z24

4z24


Resolution: 2.915→29.909 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 7578 5.01 %Thin shells
Rwork0.1652 ---
obs0.1676 151187 95.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.915→29.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40061 0 424 699 41184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941509
X-RAY DIFFRACTIONf_angle_d1.25456684
X-RAY DIFFRACTIONf_dihedral_angle_d11.37914854
X-RAY DIFFRACTIONf_chiral_restr0.0546280
X-RAY DIFFRACTIONf_plane_restr0.0077375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9147-2.94780.36171230.30393153X-RAY DIFFRACTION63
2.9478-2.98240.32881800.25274981X-RAY DIFFRACTION98
2.9824-3.01880.30425380.23794554X-RAY DIFFRACTION98
3.0188-3.0570.309680.23525062X-RAY DIFFRACTION99
3.057-3.09710.30094740.23294638X-RAY DIFFRACTION98
3.0971-3.13950.40510.22435114X-RAY DIFFRACTION98
3.1395-3.18430.2824750.21864696X-RAY DIFFRACTION98
3.1843-3.23180.011310.21415106X-RAY DIFFRACTION98
3.2318-3.28220.28634770.22084656X-RAY DIFFRACTION98
3.2822-3.3360.511520.21535095X-RAY DIFFRACTION98
3.336-3.39340.24754750.1964674X-RAY DIFFRACTION98
3.3934-3.45510.359630.19415096X-RAY DIFFRACTION98
3.4551-3.52140.25394760.19024636X-RAY DIFFRACTION98
3.5214-3.59320.259420.17815112X-RAY DIFFRACTION98
3.5932-3.67120.23644770.16854608X-RAY DIFFRACTION98
3.6712-3.75640.21863390.16824813X-RAY DIFFRACTION97
3.7564-3.85020.20631360.16254923X-RAY DIFFRACTION97
3.8502-3.9540.20474750.15424630X-RAY DIFFRACTION97
3.954-4.07010.001210.14585126X-RAY DIFFRACTION97
4.0701-4.20110.18784770.14564599X-RAY DIFFRACTION97
4.2011-4.35090.20110.13125066X-RAY DIFFRACTION96
4.3509-4.52450.16754750.12254603X-RAY DIFFRACTION97
4.5245-4.72970.124820.11855054X-RAY DIFFRACTION96
4.7297-4.97790.16574740.11874599X-RAY DIFFRACTION96
4.9779-5.28820.307820.12745077X-RAY DIFFRACTION96
5.2882-5.6940.17734750.13484593X-RAY DIFFRACTION95
5.694-7.15750.18444750.13174581X-RAY DIFFRACTION94
7.1575-29.91020.12794740.13834635X-RAY DIFFRACTION91

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