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- PDB-5v7y: Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu -

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Basic information

Entry
Database: PDB / ID: 5v7y
TitleProlyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu
Components2OG-Fe(II) oxygenase
KeywordsOXIDOREDUCTASE / Prolyl 4-hydroxylase / Dioxygenase / Cupin
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase / L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / 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 / : / IMIDAZOLE / trifluoroacetic acid / procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSchnicker, N.J. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Iowa College of Liberal Arts and Sciences United States
CitationJournal: Biochemistry / Year: 2017
Title: Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu.
Authors: Schnicker, N.J. / Razzaghi, M. / Guha Thakurta, S. / Chakravarthy, S. / Dey, M.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2OG-Fe(II) oxygenase
B: 2OG-Fe(II) oxygenase
D: 2OG-Fe(II) oxygenase
C: 2OG-Fe(II) oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,02218
Polymers98,8344
Non-polymers1,18714
Water10,845602
1
A: 2OG-Fe(II) oxygenase
B: 2OG-Fe(II) oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8647
Polymers49,4172
Non-polymers4475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 2OG-Fe(II) oxygenase
C: 2OG-Fe(II) oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,15811
Polymers49,4172
Non-polymers7409
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-47 kcal/mol
Surface area34020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.238, 106.826, 81.056
Angle α, β, γ (deg.)90.000, 103.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABDC

#1: Protein
2OG-Fe(II) oxygenase / Procollagen-Proline Dioxygenase


Mass: 24708.592 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Ala2 is from cloning / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BASH2_01493, BVB96_22550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7R8C5, UniProt: A0A4Y1WAP5*PLUS

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Non-polymers , 6 types, 616 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2HF3O2
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M imidazole pH 8.0, 5% PEG 4000, 15% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→63.4 Å / Num. obs: 51889 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.03 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.057 / Rrim(I) all: 0.108 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.05-2.110.4750.8130.2940.5699.9
8.94-63.40.0240.9990.0140.02898.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.28data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IAX
Resolution: 2.05→63.397 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.38
RfactorNum. reflection% reflection
Rfree0.2086 2601 5.02 %
Rwork0.1611 --
obs0.1635 51781 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.5 Å2 / Biso mean: 22.5702 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 2.05→63.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 68 604 7092
Biso mean--23.71 30.12 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126652
X-RAY DIFFRACTIONf_angle_d0.8769015
X-RAY DIFFRACTIONf_chiral_restr0.058988
X-RAY DIFFRACTIONf_plane_restr0.0051175
X-RAY DIFFRACTIONf_dihedral_angle_d20.4532399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.08730.2291430.187426132756100
2.0873-2.12740.25071410.189425912732100
2.1274-2.17090.22791420.189925842726100
2.1709-2.21810.27681160.188825912707100
2.2181-2.26970.27751480.18552590273899
2.2697-2.32640.23671190.18532582270199
2.3264-2.38930.22921330.17782604273799
2.3893-2.45960.28211340.17652567270199
2.4596-2.5390.2321380.17592577271599
2.539-2.62980.2681460.175926072753100
2.6298-2.73510.23971570.1725592716100
2.7351-2.85960.25241310.171625662697100
2.8596-3.01030.24021170.16426282745100
3.0103-3.19890.22361090.171426232732100
3.1989-3.44590.20781490.152568271799
3.4459-3.79260.18211420.13962583272599
3.7926-4.34130.14631400.12452559269998
4.3413-5.46910.13631330.13112586271998
5.4691-63.42710.18651630.17152602276599

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