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- PDB-4bt8: CRYSTAL STRUCTURE OF THE APO FORM OF N-TERMINAL DOMAIN AND PEPTID... -

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Basic information

Entry
Database: PDB / ID: 4bt8
TitleCRYSTAL STRUCTURE OF THE APO FORM OF N-TERMINAL DOMAIN AND PEPTIDE SUBSTRATE BINDING DOMAIN OF PROLYL-4 HYDROXYLASE TYPE I FROM HUMAN
ComponentsPROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1
KeywordsOXIDOREDUCTASE / TETRATRICOPEPTIDE REPEAT MOTIF / COILED-COIL
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
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: 2.198 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
DepositionJun 14, 2013Deposition 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 / 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
B: PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1


Theoretical massNumber of molelcules
Total (without water)55,0382
Polymers55,0382
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-58.9 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.939, 105.403, 65.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 27519.084 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) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P13674, procollagen-proline 4-dioxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.34 Å3/Da / Density % sol: 47.3 % / Description: NONE
Crystal growpH: 7.5
Details: 25-30% PEG400, 10% ISOPROPANOL, 100MM HEPES PH 7.5, 5MM SPERMINE HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→48.6 Å / Num. obs: 25805 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 46.04 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 3.85 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.3 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YQ8

2yq8


Resolution: 2.198→48.63 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 32.2 / Stereochemistry target values: ML
Details: THE NUMBERING SHOULD START WITH 0 FROM THE INITIAL METHIONINE
RfactorNum. reflection% reflection
Rfree0.2614 1301 5.1 %
Rwork0.2182 --
obs0.2204 25785 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.198→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 0 81 3772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093754
X-RAY DIFFRACTIONf_angle_d1.1825070
X-RAY DIFFRACTIONf_dihedral_angle_d14.9971414
X-RAY DIFFRACTIONf_chiral_restr0.069570
X-RAY DIFFRACTIONf_plane_restr0.006649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1978-2.28580.37011380.33952619X-RAY DIFFRACTION96
2.2858-2.38980.33261450.30832705X-RAY DIFFRACTION100
2.3898-2.51580.3561450.28982717X-RAY DIFFRACTION99
2.5158-2.67340.35961390.27942701X-RAY DIFFRACTION99
2.6734-2.87980.31371470.24612733X-RAY DIFFRACTION99
2.8798-3.16960.31191450.24062727X-RAY DIFFRACTION100
3.1696-3.62810.24561430.21142697X-RAY DIFFRACTION97
3.6281-4.57050.24141460.18262765X-RAY DIFFRACTION99
4.5705-48.64160.20971530.18852820X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.7551-0.2541-1.34720.4914-0.45992.1959-0.07940.4637-1.0491-0.0905-0.174-0.0050.41410.06680.24760.33070.02170.05930.125-0.04860.377-0.597712.1124-36.6302
21.63550.7177-0.38921.67180.12426.03031.2507-1.11340.05590.274-1.12050.302-0.54620.49980.00860.8002-0.41970.22441.2697-0.07410.3948-25.37713.6898-3.9517
36.2954-1.5824-5.04592.46641.61547.6779-0.81680.90760.14620.37130.228-0.0861.13650.03690.36991.0044-0.5079-0.14631.15530.1380.4576-17.252518.352814.7769
42.43440.98-3.89821.9856-0.55832.06820.183-0.0222-1.58750.141-0.26560.05330.1469-0.24810.16740.3105-0.00740.0250.30510.0890.5383-2.50168.1985-28.5644
53.2354-0.75942.07085.2792-1.99738.20130.2329-0.88550.19120.65440.25031.05381.3335-1.4925-0.68820.4964-0.30880.2431.03050.02390.2032-27.606313.117-18.8689
62.32313.9633-3.87372.2071-1.81281.57880.3125-1.7933-0.8130.0521-0.5664-0.36120.10590.51230.20930.25450.00430.04720.38320.05790.29983.597719.5259-29.0521
78.0829-9.8051-7.87442.12799.02788.20570.78950.81720.7616-0.4112-0.7185-1.0535-1.71440.782-0.11880.80340.17020.16290.7750.17680.461130.178116.8205-52.2147
82.0761-4.17362.37878.0242-1.46621.05210.0923-0.3132-0.7766-0.4458-0.1903-0.02040.05870.10580.27760.52970.18990.06680.7813-0.03380.439828.59951.7768-52.4391
96.96614.0603-0.01045.2955-1.65373.16950.3321.24980.4865-0.1847-0.17760.2243-0.1667-0.4917-0.16240.52990.31810.11050.80820.08710.376522.368713.3141-60.9367
108.55151.1688-7.83250.5777-0.6728.10290.53151.32430.2723-0.4027-0.1050.3430.067-0.6327-0.09620.65360.33870.08471.12290.17590.486316.299613.6687-65.2521
116.86393.7808-4.60374.8856-3.33412.1608-0.2993-1.3794-0.0892-0.8159-0.11080.06250.48050.04250.50340.83030.3898-0.04361.13040.03340.403314.348517.5213-78.1626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 7 THROUGH 106 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 107 THROUGH 201 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 202 THROUGH 238 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 7 THROUGH 62 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 63 THROUGH 75 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 76 THROUGH 106 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 107 THROUGH 123 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 124 THROUGH 146 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 147 THROUGH 178 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 179 THROUGH 201 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 202 THROUGH 238 )

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