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- PDB-3gze: Algal prolyl 4-hydroxylase complexed with zinc and (Ser-Pro)5 pep... -

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Basic information

Entry
Database: PDB / ID: 3gze
TitleAlgal prolyl 4-hydroxylase complexed with zinc and (Ser-Pro)5 peptide substrate
Components
  • Peptide substrate (Ser-Pro)5
  • Predicted protein
KeywordsHYDROLASE / jelly-roll / double-stranded beta-helix / proline-rich peptide / poly-(L-proline) type II helix
Function / homology
Function and homology information


peptidyl-proline hydroxylation to 4-hydroxy-L-proline / L-ascorbic acid binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / dioxygenase activity / iron ion binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Pistil-specific extensin-like protein / ShK toxin domain / ShK domain-like / ShKT domain / ShKT domain profile. / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase ...Pistil-specific extensin-like protein / ShK toxin domain / ShK domain-like / ShKT domain / ShKT domain profile. / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Uncharacterized protein / Vegetative cell wall protein gp1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsKoski, M.K. / Wierenga, R.K.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The Crystal Structure of an Algal Prolyl 4-Hydroxylase Complexed with a Proline-rich Peptide Reveals a Novel Buried Tripeptide Binding Motif
Authors: Koski, M.K. / Hieta, R. / Hirsila, M. / Ronka, A. / Myllyharju, J. / Wierenga, R.K.
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 19, 2014Group: Derived calculations
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted protein
B: Predicted protein
C: Predicted protein
D: Predicted protein
X: Peptide substrate (Ser-Pro)5
Y: Peptide substrate (Ser-Pro)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,45525
Polymers102,2396
Non-polymers1,21619
Water8,431468
1
A: Predicted protein
B: Predicted protein
X: Peptide substrate (Ser-Pro)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,82314
Polymers51,1203
Non-polymers70311
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-17 kcal/mol
Surface area17400 Å2
MethodPISA
2
C: Predicted protein
D: Predicted protein
Y: Peptide substrate (Ser-Pro)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,63211
Polymers51,1203
Non-polymers5138
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-17 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.250, 58.750, 105.160
Angle α, β, γ (deg.)90.000, 102.210, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Predicted protein / Prolyl 4-hydroxylase


Mass: 25090.283 Da / Num. of mol.: 4 / Fragment: N-terminally truncated construct, residues 30-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: Wild type CC125 mt+ 137c / Gene: P4H-1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: A8J7D3
#2: Protein/peptide Peptide substrate (Ser-Pro)5


Mass: 938.978 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: this is designed using the (Ser-Pro)n -region of the potential substrate of Cr-P4H-1, namely the domain 3 of the GP1 protein of the C. reinhardtii cell wall (GenBank accession code AF309494, ...Details: this is designed using the (Ser-Pro)n -region of the potential substrate of Cr-P4H-1, namely the domain 3 of the GP1 protein of the C. reinhardtii cell wall (GenBank accession code AF309494, Ferris et al. 2001, Biochemistry 40:2978-2987).
Source: (synth.) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9FPQ6*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 295 K / Method: microbatch under-oil / pH: 5.5
Details: 5% PEG Smear, 0.1M acetate, 10mM zinc acetate, pH 5.5, Microbatch under-oil, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.98→25 Å / Num. all: 75581 / Num. obs: 68688 / % possible obs: 93.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 24.62 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.16
Reflection shellResolution: 1.98→2.04 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.3 / Num. unique all: 4412 / % possible all: 87.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V4A

2v4a


Resolution: 1.98→20.6 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.188 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25392 3434 5 %RANDOM
Rwork0.21704 ---
obs0.21888 65243 93.45 %-
all-68677 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.741 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å21.98 Å2
2---0.2 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.98→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6345 0 34 468 6847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226654
X-RAY DIFFRACTIONr_bond_other_d0.0020.024526
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.959039
X-RAY DIFFRACTIONr_angle_other_deg2.263311088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48724.444288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.734151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4181526
X-RAY DIFFRACTIONr_chiral_restr0.1010.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217377
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021277
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.54099
X-RAY DIFFRACTIONr_mcbond_other0.2421.51656
X-RAY DIFFRACTIONr_mcangle_it1.39326620
X-RAY DIFFRACTIONr_scbond_it2.28932555
X-RAY DIFFRACTIONr_scangle_it3.3274.52413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.984→2.035 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 232 -
Rwork0.253 4406 -
all-4638 -
obs--86.81 %
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)
11.6836-0.3958-0.24550.93730.26890.8489-0.0207-0.00250.04420.00730.0343-0.0387-0.02520.0592-0.0136-0.0113-0.0024-0.01650.02630.00070.0305-18.4249.3846.558
21.0706-0.0867-0.48711.3016-0.09161.50540.0002-0.13270.12830.1046-0.00340.0443-0.27110.12810.00320.0632-0.0162-0.01680.0556-0.01070.0678-37.35132.22618.55
31.4806-0.4655-0.5540.68780.14761.3340.0105-0.10230.04110.0040.0352-0.03710.0411-0.0013-0.04570.0553-0.00080.03680.05620.0060.0371-83.75937.72540.153
41.81490.0186-0.11151.27120.12420.64170.016-0.214-0.29980.0723-0.0173-0.0350.23530.01630.00130.10860.00250.02790.08950.04350.0936-62.93314.62931.98
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 250
2X-RAY DIFFRACTION1X4 - 9
3X-RAY DIFFRACTION1A1
4X-RAY DIFFRACTION1A254
5X-RAY DIFFRACTION2B37 - 250
6X-RAY DIFFRACTION2B2
7X-RAY DIFFRACTION2B254
8X-RAY DIFFRACTION3C38 - 250
9X-RAY DIFFRACTION3Y2 - 9
10X-RAY DIFFRACTION3C3
11X-RAY DIFFRACTION3C254
12X-RAY DIFFRACTION4D37 - 249
13X-RAY DIFFRACTION4D4
14X-RAY DIFFRACTION4D254

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