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- PDB-2jij: Crystal structure of the apo form of Chlamydomonas reinhardtii pr... -

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Basic information

Entry
Database: PDB / ID: 2jij
TitleCrystal structure of the apo form of Chlamydomonas reinhardtii prolyl- 4 hydroxylase type I
ComponentsPROLYL-4 HYDROXYLASE
KeywordsHYDROLASE
Function / homologyq2cbj1_9rhob like domain / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesCHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / Version format compliance
Revision 1.2Dec 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 / struct_ncs_dom_lim / struct_site
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 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
C: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5195
Polymers78,4483
Non-polymers712
Water55831
1
A: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1852
Polymers26,1491
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROLYL-4 HYDROXYLASE


Theoretical massNumber of molelcules
Total (without water)26,1491
Polymers26,1491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PROLYL-4 HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1852
Polymers26,1491
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.320, 117.460, 72.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA28 - 328 - 12
21METMETGLYGLYBB28 - 328 - 12
31METMETGLYGLYCC28 - 328 - 12
12TRPTRPMETMETAA38 - 7418 - 54
22TRPTRPMETMETBB38 - 7418 - 54
32TRPTRPMETMETCC38 - 7418 - 54
13THRTHRHISHISAA96 - 13376 - 113
23THRTHRHISHISBB96 - 13376 - 113
33THRTHRHISHISCC96 - 13376 - 113
14ASPASPTHRTHRAA149 - 171129 - 151
24ASPASPTHRTHRBB149 - 171129 - 151
34ASPASPTHRTHRCC149 - 171129 - 151
15GLUGLUVALVALAA177 - 187157 - 167
25GLUGLUVALVALBB177 - 187157 - 167
35GLUGLUVALVALCC177 - 187157 - 167
16SERSERTHRTHRAA193 - 232173 - 212
26SERSERTHRTHRBB193 - 232173 - 212
36SERSERTHRTHRCC193 - 232173 - 212
17TRPTRPILEILEAA238 - 249218 - 229
27TRPTRPILEILEBB238 - 249218 - 229
37TRPTRPILEILECC238 - 249218 - 229

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Components

#1: Protein PROLYL-4 HYDROXYLASE


Mass: 26149.494 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM V29. CONTAINS ALSO N-TERMINAL HIS-TAG.
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Strain: CC125MT137C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI(DE3)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINALLY TRUNCATED CONSTRUCT STARTING FROM V29. ENGINEERED MUTATION T28M

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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: 49 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. obs: 69167 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / % possible all: 99

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Processing

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

2v4a


Resolution: 2.9→33.83 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.873 / SU B: 32.955 / SU ML: 0.287 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 960 5.1 %RANDOM
Rwork0.212 ---
obs0.214 17898 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--0.76 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 2 31 4673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224764
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.9496447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.575581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62424.265204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47415806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8721519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023583
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21993
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23139
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.52968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85524704
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.02532041
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5954.51743
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A664tight positional0.060.05
2B664tight positional0.050
3C664tight positional0.060
1A628medium positional0.070.5
2B628medium positional0.060
3C628medium positional0.070
1A664tight thermal0.110.5
2B664tight thermal0.110
3C664tight thermal0.110
1A628medium thermal0.132
2B628medium thermal0.120
3C628medium thermal0.110
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 76
Rwork0.304 1286
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)
15.1618-0.80651.10883.0958-0.74992.9744-0.1395-0.250.36290.1820.06590.0729-0.3931-0.27780.0736-0.1846-0.00120.0081-0.16370.015-0.182417.152620.76618.9913
24.12510.6524-0.05023.4023-1.5082.5222-0.14710.4024-0.0526-0.2040.0939-0.18180.13080.09180.0532-0.1813-0.02130.0073-0.2138-0.0138-0.097347.386615.92139.7792
34.9405-0.13670.74851.74190.07324.98530.0011-0.52490.24380.302-0.2672-0.3116-0.11990.31990.2661-0.0142-0.1354-0.01710.06510.088-0.108114.69025.322547.6934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 251
2X-RAY DIFFRACTION2B28 - 250
3X-RAY DIFFRACTION3C28 - 249

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