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- PDB-5hv4: Crystal Structure of a Prolyl 4-Hydroxylase Complexed with Alpha-... -

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Basic information

Entry
Database: PDB / ID: 5hv4
TitleCrystal Structure of a Prolyl 4-Hydroxylase Complexed with Alpha-ketoglutarate from the Pathogenic Bacterium Bacillus anthracis in C2221
Components2OG-Fe(II) oxygenase
KeywordsOXIDOREDUCTASE / P4H / Dioxygenase / Cupin / Fe(II)/alpha-ketoglutarate
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase activity / L-ascorbic acid binding / iron ion binding
Similarity search - Function
Prolyl 4-hydroxylase / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / Prolyl 4-hydroxylase, alpha subunit domain protein / Prolyl 4-hydroxylase, alpha subunit domain protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSchnicker, N.J. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
College of Liberal Arts and Sciences University of Iowa United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural analysis of cofactor binding for a prolyl 4-hydroxylase from the pathogenic bacterium Bacillus anthracis.
Authors: Schnicker, N.J. / Dey, M.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 27, 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 / pdbx_struct_oper_list / 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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_struct_oper_list.symmetry_operation / _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: 2OG-Fe(II) oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,65113
Polymers24,7091
Non-polymers94312
Water1,910106
1
A: 2OG-Fe(II) oxygenase
hetero molecules

A: 2OG-Fe(II) oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,30326
Polymers49,4172
Non-polymers1,88524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)42.551, 146.189, 75.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 2OG-Fe(II) oxygenase / 2OG-Fe(II) oxygenase superfamily protein / Prolyl 4-hydroxylase / alpha subunit domain protein


Mass: 24708.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium)
Gene: GBAA_4459, AB163_21210, AB164_16730, AB165_11640, AB166_03610, AB167_21505, AB168_05660, AB169_05325, AB170_09560, AB171_10145, AB893_21665, ADK17_22720, ADK18_21540, ADT20_05380, ADT21_14515, BF27_3254
Production host: Escherichia coli (E. coli) / References: UniProt: Q81LZ8, UniProt: A0A4Y1WAP5*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAuthors state that this is a cloning artifact from the restriction site.

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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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES pH 7.8, 0.05 M Cadmium sulfate, 0.9 M Sodium acetate tri-hydrate, 0.1 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→52.372 Å / Num. obs: 10150 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 24.68 Å2 / Rsym value: 0.098 / Net I/σ(I): 15.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ITQ

3itq


Resolution: 2.35→52.37 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 495 4.89 %
Rwork0.199 --
obs0.201 10133 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→52.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 21 106 1644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061587
X-RAY DIFFRACTIONf_angle_d0.5182140
X-RAY DIFFRACTIONf_dihedral_angle_d15.123927
X-RAY DIFFRACTIONf_chiral_restr0.042235
X-RAY DIFFRACTIONf_plane_restr0.002278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.58650.29241060.21032359X-RAY DIFFRACTION100
2.5865-2.96070.24371320.20642366X-RAY DIFFRACTION100
2.9607-3.73010.21711340.19372396X-RAY DIFFRACTION100
3.7301-52.38480.25441230.19622517X-RAY DIFFRACTION100

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