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- PDB-6a4x: Oxidase ChaP-H2 -

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Basic information

Entry
Database: PDB / ID: 6a4x
TitleOxidase ChaP-H2
ComponentsBleomycin resistance protein
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 / metal ion binding / : / Bleomycin resistance protein
Function and homology information
Biological speciesStreptomyces curacoi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZhang, B. / Wang, Y.S. / 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 1.2Nov 22, 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 / 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_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.ptnr2_symmetry / _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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bleomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4252
Polymers14,3691
Non-polymers561
Water3,153175
1
A: Bleomycin resistance protein
hetero molecules

A: Bleomycin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8494
Polymers28,7382
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3700 Å2
ΔGint-49 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.870, 76.870, 47.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Bleomycin resistance protein / dioxygenase


Mass: 14368.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces curacoi (bacteria) / Gene: AQI70_17615 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A124H109
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: ammonium acetate, sodium citrate tribasic dihydrate, PEG 4000

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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: 1.63→40.2 Å / Num. obs: 18139 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 20.21 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Net I/σ(I): 13 / Num. measured all: 127616 / Scaling rejects: 326
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.63-1.667.20.90762468660.7540.3560.9772.199.9
8.93-40.25.80.058401450.980.0260.0563399.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
TRUNCATEdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A4Z

6a4z


Resolution: 1.63→40.2 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.23
RfactorNum. reflection% reflection
Rfree0.2127 892 5.12 %
Rwork0.1857 --
obs0.187 17434 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.35 Å2 / Biso mean: 28.9711 Å2 / Biso min: 13.18 Å2
Refinement stepCycle: final / Resolution: 1.63→40.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 1 175 1173
Biso mean--32.78 37.55 -
Num. residues----127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6301-1.73230.25941420.23792544268691
1.7323-1.8660.24881370.21652585272292
1.866-2.05380.24741640.18272743290797
2.0538-2.3510.2051420.17592775291798
2.351-2.96180.20381490.19442868301798
2.9618-40.21630.20011580.176130273185100
Refinement TLS params.Method: refined / Origin x: 5.1579 Å / Origin y: 17.6335 Å / Origin z: 5.4247 Å
111213212223313233
T0.1557 Å2-0.004 Å20.007 Å2-0.1554 Å20.0215 Å2--0.1543 Å2
L1.951 °2-1.0153 °20.4036 °2-2.3628 °20.0038 °2--1.0751 °2
S-0.1046 Å °-0.0879 Å °-0.0711 Å °0.1832 Å °0.1056 Å °0.2087 Å °-0.0159 Å °-0.0594 Å °0.0158 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 127
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allS1 - 175

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