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- PDB-4mm0: Crystal Structure Analysis of the Putative Thioether Synthase Sgv... -

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Basic information

Entry
Database: PDB / ID: 4mm0
TitleCrystal Structure Analysis of the Putative Thioether Synthase SgvP Involved in the Tailoring Step of Griseoviridin
ComponentsP450-like monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / p450-like monooxygenase
Similarity search - Component
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, H. / Huang, L. / Yi, M. / Cai, T. / Zhang, H.
CitationJournal: To be Published
Title: Structural Analysis of SgvP: a Putative Thioether Synthase Involved in the Tailoring Step of Griseoviridin
Authors: Zhang, H. / Huang, L. / Yi, M. / Cai, T. / Zhang, H.
History
DepositionSep 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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: P450-like monooxygenase
B: P450-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0414
Polymers87,8082
Non-polymers1,2332
Water6,900383
1
A: P450-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5202
Polymers43,9041
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: P450-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5202
Polymers43,9041
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.050, 184.050, 80.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein P450-like monooxygenase


Mass: 43903.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoviridis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: R9USI6*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of ...References: UniProt: R9USI6*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT. THE SEQUENCE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT. THE SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH ACCESSION NUMBER AGN74891.1. N-TERMINAL RESIDUES MET-ALA-SER ARE FROM EXPRESSION TAGS.

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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: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 20%(w/v) Polyethylene glycol 3350, 0.2M Potassium sodium tartrate tetrahydrate, 3.0%(v/v) Dimethyl sulfoxide, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 77.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979228 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979228 Å / Relative weight: 1
ReflectionResolution: 2.6→29.856 Å / Num. all: 43006 / Num. obs: 42958 / % possible obs: 99.89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.11
Reflection shellResolution: 2.6→2.67 Å / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y46

2y46


Resolution: 2.6→29.856 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 2.03 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 2166 5.05 %RANDOM
Rwork0.1706 ---
all0.1774 42905 --
obs0.1727 42905 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.81 Å2 / Biso mean: 30.0195 Å2 / Biso min: 4.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6091 0 86 383 6560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086323
X-RAY DIFFRACTIONf_angle_d1.1278647
X-RAY DIFFRACTIONf_dihedral_angle_d13.6992339
X-RAY DIFFRACTIONf_chiral_restr0.066974
X-RAY DIFFRACTIONf_plane_restr0.0051132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6002-2.66060.31851560.222226672823
2.6606-2.72710.2791430.209726392782
2.7271-2.80080.24181220.196927032825
2.8008-2.88320.26171470.193126762823
2.8832-2.97610.2481690.190626642833
2.9761-3.08240.27161440.191326812825
3.0824-3.20570.23771280.184327002828
3.2057-3.35140.23591280.181427132841
3.3514-3.52780.24761740.173826662840
3.5278-3.74850.22451330.175226922825
3.7485-4.03720.20661380.161327362874
4.0372-4.44230.18191490.145327312880
4.4423-5.08240.17441420.1427512893
5.0824-6.3930.19851280.178828062934
6.393-29.85760.1611650.156529143079

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