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- PDB-6j85: Crystal structure of HinD apo -

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Basic information

Entry
Database: PDB / ID: 6j85
TitleCrystal structure of HinD apo
ComponentsNocardicin N-oxygenase
KeywordsOXIDOREDUCTASE / P450 / indolactam / oxidation
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Nocardicin N-oxygenase
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFei, H. / Mori, T. / Abe, I.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Molecular basis for the P450-catalyzed C-N bond formation in indolactam biosynthesis.
Authors: He, F. / Mori, T. / Morita, I. / Nakamura, H. / Alblova, M. / Hoshino, S. / Awakawa, T. / Abe, I.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _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
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Nocardicin N-oxygenase
B: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0844
Polymers95,8512
Non-polymers1,2332
Water4,972276
1
A: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5422
Polymers47,9261
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-26 kcal/mol
Surface area16540 Å2
MethodPISA
2
B: Nocardicin N-oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5422
Polymers47,9261
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-26 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.356, 152.647, 56.394
Angle α, β, γ (deg.)90.00, 115.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nocardicin N-oxygenase


Mass: 47925.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria)
Gene: SAMN05444320_102263 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M4Y7D5
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 276 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES (pH 6.5) containing 1200 mM (NH4)2HPO4 and 100 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.16 Å / Num. obs: 37990 / % possible obs: 99.9 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3318 / CC1/2: 0.652 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J82

6j82


Resolution: 2.2→48.157 Å / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 30.15
RfactorNum. reflection% reflection
Rfree0.226 2011 5.3 %
Rwork0.1701 --
obs0.1819 37956 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 0 86 276 6566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086450
X-RAY DIFFRACTIONf_angle_d0.9828834
X-RAY DIFFRACTIONf_dihedral_angle_d4.1333870
X-RAY DIFFRACTIONf_chiral_restr0.0511000
X-RAY DIFFRACTIONf_plane_restr0.0071150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.25530.2941490.23112616X-RAY DIFFRACTION95
2.2553-2.31620.25811360.22882489X-RAY DIFFRACTION95
2.3162-2.38440.29671380.22042576X-RAY DIFFRACTION95
2.3844-2.46130.35911460.2162591X-RAY DIFFRACTION94
2.4613-2.54930.3011430.21612534X-RAY DIFFRACTION95
2.5493-2.65130.27371430.2042556X-RAY DIFFRACTION95
2.6513-2.77190.24941430.19952581X-RAY DIFFRACTION95
2.7719-2.9180.28771420.19412552X-RAY DIFFRACTION95
2.918-3.10070.25321480.18462588X-RAY DIFFRACTION94
3.1007-3.33990.22681410.17322567X-RAY DIFFRACTION95
3.3399-3.67560.22021440.15532529X-RAY DIFFRACTION94
3.6756-4.20660.18681450.14312578X-RAY DIFFRACTION95
4.2066-5.29640.19181440.13942583X-RAY DIFFRACTION94
5.2964-33.46480.22671460.18192589X-RAY DIFFRACTION94

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