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- PDB-2yq8: Crystal structure of the SeMet-labeled N-terminal domain and pept... -

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Basic information

Entry
Database: PDB / ID: 2yq8
TitleCrystal structure of the SeMet-labeled N-terminal domain and peptide substrate binding domain of alpha subunit of prolyl-4 hydroxylase type I from human.
ComponentsPROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase complex / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / collagen fibril organization / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum ...procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase complex / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / collagen fibril organization / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum / mitochondrion / identical protein binding / membrane
Similarity search - Function
Helix Hairpins - #1460 / Prolyl 4-hydroxylase alpha-subunit, N-terminal / Prolyl 4-Hydroxylase alpha-subunit, N-terminal region / Prolyl 4-hydroxylase peptide-substrate-binding domain / 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. / Oxoglutarate/iron-dependent dioxygenase ...Helix Hairpins - #1460 / Prolyl 4-hydroxylase alpha-subunit, N-terminal / Prolyl 4-Hydroxylase alpha-subunit, N-terminal region / Prolyl 4-hydroxylase peptide-substrate-binding domain / 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. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Tetratricopeptide repeat domain / Helix Hairpins / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Helix non-globular / Special / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Prolyl 4-hydroxylase subunit alpha-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.987 Å
AuthorsAnantharajan, J. / Koski, M.K. / Wierenga, R.K.
CitationJournal: Structure / Year: 2013
Title: The Structural Motifs for Substrate Binding and Dimerization of the Alpha Subunit of Collagen Prolyl 4-Hydroxylase
Authors: Anantharajan, J. / Koski, M.K. / Kursula, P. / Hieta, R. / Bergmann, U. / Myllyharju, J. / Wierenga, R.K.
History
DepositionNov 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references / Structure summary
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 25, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
B: PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1


Theoretical massNumber of molelcules
Total (without water)55,6012
Polymers55,6012
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-54.7 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.878, 72.017, 66.431
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1 / 4-PH ALPHA-1 / PROCOLLAGEN-PROLINE\ / 2-OXOGLUTARATE-4-DIOXYGENASE SUBUNIT ALPHA-1 / PROLYL-4 ...4-PH ALPHA-1 / PROCOLLAGEN-PROLINE\ / 2-OXOGLUTARATE-4-DIOXYGENASE SUBUNIT ALPHA-1 / PROLYL-4 HYDROXYLASE TYPE I


Mass: 27800.457 Da / Num. of mol.: 2 / Fragment: COLLAGEN BINDING DOMAIN, RESIDUES 18-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: P13674, procollagen-proline 4-dioxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 8.5
Details: 26-29% PEGMME 2000, 200MM KSCN AND 5MM DTT, 5MM SPERMINE TETRAHYDROCHLORIDE, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9737
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 2.99→45 Å / Num. obs: 19064 / % possible obs: 96.7 % / Observed criterion σ(I): 2.9 / Redundancy: 3.4 % / Biso Wilson estimate: 52.28 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.23
Reflection shellResolution: 2.99→3.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 73.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5F

2v5f


Resolution: 2.987→44.622 Å / SU ML: 0.43 / σ(F): 1.37 / Phase error: 30.37 / Stereochemistry target values: ML
Details: RESIDUES 1-6, 138-143, 238 IN CHAIN A & RESIDUES 1-6, 138-142, 238 IN CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2774 954 5 %
Rwork0.2089 --
obs0.2124 19054 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.9 Å2
Refinement stepCycle: LAST / Resolution: 2.987→44.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 0 9 3661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123714
X-RAY DIFFRACTIONf_angle_d1.5025016
X-RAY DIFFRACTIONf_dihedral_angle_d16.2761396
X-RAY DIFFRACTIONf_chiral_restr0.088565
X-RAY DIFFRACTIONf_plane_restr0.005641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9875-3.14490.38131190.27582150X-RAY DIFFRACTION80
3.1449-3.34190.32891400.24962598X-RAY DIFFRACTION98
3.3419-3.59990.30571340.21942663X-RAY DIFFRACTION100
3.5999-3.96190.28171410.19612695X-RAY DIFFRACTION100
3.9619-4.53470.26711410.1972664X-RAY DIFFRACTION100
4.5347-5.71140.25681360.19822670X-RAY DIFFRACTION100
5.7114-44.62670.23881430.19572660X-RAY DIFFRACTION100

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