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- PDB-2jig: Crystal structure of Chlamydomonas reinhardtii prolyl-4 hydroxyla... -

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Basic information

Entry
Database: PDB / ID: 2jig
TitleCrystal structure of Chlamydomonas reinhardtii prolyl-4 hydroxylase type I complexed with zinc and pyridine-2,4-dicarboxylate
ComponentsPROLYL-4 HYDROXYLASE
KeywordsHYDROLASE
Function / homologyq2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta / PYRIDINE-2,4-DICARBOXYLIC ACID
Function and homology information
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKoski, M.K. / Hieta, R. / Bollner, C. / Kivirikko, K.I. / Myllyharju, J. / Wierenga, R.K.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Active Site of an Algal Prolyl 4-Hydroxylase Has a Large Structural Plasticity.
Authors: Koski, M.K. / Hieta, R. / Bollner, C. / Kivirikko, K.I. / Myllyharju, J. / Wierenga, R.K.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / 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 / _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_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.value / _struct_conn.pdbx_dist_value / _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_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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)50,5359
Polymers49,9182
Non-polymers6177
Water7,837435
1
A: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4456
Polymers24,9591
Non-polymers4865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0903
Polymers24,9591
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.920, 60.250, 116.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROLYL-4 HYDROXYLASE


Mass: 24959.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM G30 / Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Strain: CC125MT137C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI(DE3)

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Non-polymers , 5 types, 442 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsN-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM G30

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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: 1.8 Å3/Da / Density % sol: 30 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8997
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8997 Å / Relative weight: 1
ReflectionResolution: 1.85→32 Å / Num. obs: 152984 / % possible obs: 98.1 % / Observed criterion σ(I): 2.5 / Redundancy: 2.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.3
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0028refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V4A

2v4a


Resolution: 1.85→29.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.862 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1753 5 %RANDOM
Rwork0.183 ---
obs0.186 33301 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 27 435 3687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213334
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9534518
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80424.558147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05115558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4331513
X-RAY DIFFRACTIONr_chiral_restr0.080.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022535
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21600
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22199
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6981.52090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06623281
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.66731439
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5354.51237
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 116
Rwork0.249 2217
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)
10.48450.0420.3290.85580.32021.5005-0.0091-0.03210.015-0.0417-0.05480.0179-0.0424-0.05540.0639-0.01170.0108-0.0059-0.077-0.0057-0.12270.12321.564-18.873
21.2248-0.1727-0.16911.51640.15221.0660.0056-0.19450.01010.155-0.00780.08410.0126-0.0710.00220.0225-0.0137-0.0071-0.0075-0.0042-0.14853.5334.50111.097
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 251
2X-RAY DIFFRACTION2B36 - 251

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