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- PDB-6a52: Oxidase ChaP-H1 -

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Basic information

Entry
Database: PDB / ID: 6a52
TitleOxidase ChaP-H1
Componentsdioxidase ChaP-H1
KeywordsBIOSYNTHETIC PROTEIN / VOC family / dioxygenase / dimer / Chartreusin / Oxidative Rearrangement
Function / homologyGlyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / : / Dioxidase ChaP-H1
Function and homology information
Biological speciesRhodococcus phenolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsZhang, B. / Ge, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21572100, 81522042, 81773591, 81421091, 81500059, 81673333, 21672101, and 21661140001 China
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Molecular Basis for the Final Oxidative Rearrangement Steps in Chartreusin Biosynthesis.
Authors: Wang, Y.S. / Zhang, B. / Zhu, J. / Yang, C.L. / Guo, Y. / Liu, C.L. / Liu, F. / Huang, H. / Zhao, S. / Liang, Y. / Jiao, R.H. / Tan, R.X. / Ge, H.M.
History
DepositionJun 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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: dioxidase ChaP-H1
B: dioxidase ChaP-H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1974
Polymers28,0852
Non-polymers1122
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-38 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.610, 49.940, 59.330
Angle α, β, γ (deg.)90.00, 96.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein dioxidase ChaP-H1


Mass: 14042.517 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus phenolicus (bacteria) / Strain: DSM 44812 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A3F2YLV5*PLUS
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (NH4)2SO4, MES monohydrate, polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97916 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2→49.9 Å / Num. obs: 15603 / % possible obs: 90.6 % / Redundancy: 2.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.111 / Rrim(I) all: 0.157 / Net I/σ(I): 4.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1189 / CC1/2: 0.741 / Rpim(I) all: 0.415 / Rrim(I) all: 0.59

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2→43.304 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.36
RfactorNum. reflection% reflection
Rfree0.2501 1562 10.01 %
Rwork0.1936 --
obs0.1992 15603 90.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 2 188 2124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071990
X-RAY DIFFRACTIONf_angle_d0.8652704
X-RAY DIFFRACTIONf_dihedral_angle_d10.0391150
X-RAY DIFFRACTIONf_chiral_restr0.055273
X-RAY DIFFRACTIONf_plane_restr0.007371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.06460.28111440.24471295X-RAY DIFFRACTION94
2.0646-2.13840.28361480.23441319X-RAY DIFFRACTION93
2.1384-2.2240.28931400.22331273X-RAY DIFFRACTION90
2.224-2.32520.29311400.22031252X-RAY DIFFRACTION90
2.3252-2.44780.30811370.23041232X-RAY DIFFRACTION87
2.4478-2.60120.31811230.22471115X-RAY DIFFRACTION79
2.6012-2.8020.27191510.20911352X-RAY DIFFRACTION96
2.802-3.08390.26781510.20691360X-RAY DIFFRACTION96
3.0839-3.52990.23161490.17821346X-RAY DIFFRACTION94
3.5299-4.44670.18731410.15441263X-RAY DIFFRACTION89
4.4467-43.31410.22011380.16581234X-RAY DIFFRACTION84
Refinement TLS params.Method: refined / Origin x: 11.3535 Å / Origin y: 6.6643 Å / Origin z: 16.5979 Å
111213212223313233
T0.2211 Å20.013 Å20.0516 Å2-0.1598 Å2-0.0116 Å2--0.2238 Å2
L0.8693 °20.2692 °2-0.4711 °2-1.4337 °2-0.3264 °2--1.298 °2
S-0.0104 Å °0.0982 Å °-0.0314 Å °-0.2475 Å °0.001 Å °-0.1074 Å °-0.011 Å °0.0199 Å °-0.0106 Å °
Refinement TLS groupSelection details: all

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