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- PDB-5hv0: Structural Analysis of Cofactor Binding of a Prolyl 4-Hydroxylase... -

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Basic information

Entry
Database: PDB / ID: 5hv0
TitleStructural Analysis of Cofactor Binding of a Prolyl 4-Hydroxylase from the Pathogenic Bacterium Bacillus anthracis
ComponentsProlyl 4-Hydroxylase
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: 1.63 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prolyl 4-Hydroxylase
B: Prolyl 4-Hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50621
Polymers49,4172
Non-polymers2,08919
Water7,674426
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.336, 90.336, 51.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-302-

CD

21A-303-

CD

31A-538-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 24708.592 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Production host: Escherichia coli (E. coli) / References: UniProt: Q81LZ8, UniProt: A0A4Y1WAP5*PLUS

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Non-polymers , 5 types, 445 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.11 %
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: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→39.117 Å / Num. all: 58550 / Num. obs: 58550 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 15.38 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.071 / Rsym value: 0.055 / Net I/av σ(I): 9.823 / Net I/σ(I): 20 / Num. measured all: 322968
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.63-1.725.10.4141.81100
1.72-1.825.50.2742.61100
1.82-1.955.60.1863.71100
1.95-2.15.60.1066.8199.9
2.1-2.315.70.06710.9199.9
2.31-2.585.70.05213.71100
2.58-2.985.70.04116.8199.9
2.98-3.645.50.03318.51100
3.64-5.155.50.03218.4199.6
5.15-39.1175.40.03119.2198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ITQ

3itq


Resolution: 1.63→39.117 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 2961 5.08 %
Rwork0.1739 --
obs0.1759 58323 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.63→39.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 47 426 3629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0253338
X-RAY DIFFRACTIONf_angle_d0.8414530
X-RAY DIFFRACTIONf_dihedral_angle_d19.5711195
X-RAY DIFFRACTIONf_chiral_restr0.078490
X-RAY DIFFRACTIONf_plane_restr0.004583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.65670.25881270.22352608X-RAY DIFFRACTION98
1.6567-1.68530.26911290.20122609X-RAY DIFFRACTION98
1.6853-1.7160.22571370.20242600X-RAY DIFFRACTION98
1.716-1.7490.2521400.20062589X-RAY DIFFRACTION99
1.749-1.78470.23961330.19692662X-RAY DIFFRACTION99
1.7847-1.82350.24831300.18972701X-RAY DIFFRACTION100
1.8235-1.86590.21861180.18792588X-RAY DIFFRACTION100
1.8659-1.91250.23631320.18912679X-RAY DIFFRACTION100
1.9125-1.96420.24031460.18852668X-RAY DIFFRACTION100
1.9642-2.0220.23231860.18782562X-RAY DIFFRACTION100
2.022-2.08730.21061300.17942690X-RAY DIFFRACTION100
2.0873-2.16190.23311080.17442668X-RAY DIFFRACTION100
2.1619-2.24850.23081840.17592622X-RAY DIFFRACTION100
2.2485-2.35080.23741450.16942659X-RAY DIFFRACTION100
2.3508-2.47470.21981540.17482616X-RAY DIFFRACTION100
2.4747-2.62970.23041350.18142642X-RAY DIFFRACTION100
2.6297-2.83270.221560.18112641X-RAY DIFFRACTION100
2.8327-3.11770.22041440.17572636X-RAY DIFFRACTION100
3.1177-3.56850.19431340.16272659X-RAY DIFFRACTION100
3.5685-4.49490.1811740.14292618X-RAY DIFFRACTION100
4.4949-39.12790.18431190.1662645X-RAY DIFFRACTION99

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