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- PDB-2v5f: Crystal structure of wild type peptide-binding domain of human ty... -

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Basic information

Entry
Database: PDB / ID: 2v5f
TitleCrystal structure of wild type peptide-binding domain of human type I collagen prolyl 4-hydroxylase.
Components
  • HEXA-HISTIDINE PEPTIDE
  • PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
KeywordsOXIDOREDUCTASE / ENDOPLASMIC RETICULUM / METAL-BINDING
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 / collagen fibril organization / L-ascorbic acid binding / 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 / collagen fibril organization / L-ascorbic acid binding / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum / mitochondrion / identical protein binding / membrane
Similarity search - Function
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. ...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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPekkala, M. / Hieta, R. / Kivirikko, K. / Myllyharju, J. / Wierenga, R.
CitationJournal: To be Published
Title: Crystal Structure of Wild Type Peptide-Binding Domain of Human Type I Collagen Prolyl 4- Hydroxylase.
Authors: Pekkala, M. / Hieta, R. / Kivirikko, K. / Myllyharju, J. / Wierenga, R.
History
DepositionOct 6, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 21, 2016Group: Source and taxonomy / Structure summary
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
X: HEXA-HISTIDINE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)12,9252
Polymers12,9252
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-2.5 kcal/mol
Surface area7420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.472, 59.046, 61.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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


Mass: 12078.583 Da / Num. of mol.: 1
Fragment: PEPTIDE-SUBSTRATE-BINDING DOMAIN, RESIDUES 161-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: ALPHA-1F144-S244 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P13674, procollagen-proline 4-dioxygenase
#2: Protein/peptide HEXA-HISTIDINE PEPTIDE


Mass: 846.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: ALPHA-1F144-S244 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.63 Å3/Da / Density % sol: 53.25 % / Description: NONE
Crystal growpH: 9.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1 M NA CITRATE, 100 MM CHES, PH 9.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→42.6 Å / Num. obs: 9304 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 10.1 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TJC

1tjc


Resolution: 2.03→42.65 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.996 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.265 432 5 %RANDOM
Rwork0.196 ---
obs0.199 8227 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.03→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 0 136 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021879
X-RAY DIFFRACTIONr_bond_other_d0.0020.02573
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9451186
X-RAY DIFFRACTIONr_angle_other_deg2.01331402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.7255101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89125.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47415156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.693152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02969
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02176
X-RAY DIFFRACTIONr_nbd_refined0.0610.2236
X-RAY DIFFRACTIONr_nbd_other0.0750.2598
X-RAY DIFFRACTIONr_nbtor_refined00.2417
X-RAY DIFFRACTIONr_nbtor_other00.2441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9215510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9477813
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3915369
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5797373
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.453 22
Rwork0.302 413
Refinement TLS params.Method: refined / Origin x: -0.055 Å / Origin y: 7.096 Å / Origin z: 10.14 Å
111213212223313233
T0.1316 Å20.0157 Å2-0.0016 Å2-0.0975 Å20.01 Å2--0.0204 Å2
L2.1054 °21.2983 °20.0233 °2-4.9557 °2-0.531 °2--1.581 °2
S0.0328 Å °-0.1132 Å °0.029 Å °-0.008 Å °-0.0145 Å °0.1099 Å °0.0399 Å °0.0433 Å °-0.0183 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A143 - 240
2X-RAY DIFFRACTION1X-1 - 4

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