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- PDB-1up8: Recombinant vanadium-dependent bromoperoxidase from red algae Cor... -

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Basic information

Entry
Database: PDB / ID: 1up8
TitleRecombinant vanadium-dependent bromoperoxidase from red algae Corallina pilulifera
ComponentsVANADIUM-DEPENDENT BROMOPEROXIDASE 1
KeywordsHALOPEROXIDASE / VANADATE
Function / homology
Function and homology information


bromide peroxidase / bromide peroxidase activity / metal ion binding
Similarity search - Function
Vanadium-containing Chloroperoxidase, domain 2 / Vanadium-containing Chloroperoxidase; domain 2 / Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Vanadium-dependent bromoperoxidase
Similarity search - Component
Biological speciesCORALLINA PILULIFERA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGarcia-Rodriguez, E. / Isupov, M. / Ohshiro, T. / Izumi, Y. / Littlechild, J.A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2005
Title: Enhancing Effect of Calcium and Vanadium Ions on Thermal Stability of Bromoperoxidase from Corallina Pilulifera.
Authors: Garcia-Rodriguez, E. / Ohshiro, T. / Aibara, T. / Izumi, Y. / Littlechild, J.
#1: Journal: Protein Sci. / Year: 2004
Title: Modification of Halogen Specificity of a Vanadium-Dependent Bromoperoxidase.
Authors: Ohshiro, T. / Littlechild, J. / Garcia-Rodriguez, E. / Isupov, M.N. / Iida, Y. / Kobayashi, T. / Izumi, Y.
#2: Journal: Coord Chem Rev / Year: 2003
Title: Structural Studies on the Dodecameric Vanadium Bromoperoxidase from Corallina Species
Authors: Littlechild, J. / Garcia-Rodriguez, E.
History
DepositionSep 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _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.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 / _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

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Assembly

Deposited unit
A: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
B: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
C: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
D: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,05624
Polymers261,3764
Non-polymers1,68020
Water41,9392328
1
A: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
B: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
C: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
D: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
hetero molecules

A: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
B: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
C: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
D: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
hetero molecules

A: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
B: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
C: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
D: VANADIUM-DEPENDENT BROMOPEROXIDASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)789,16772
Polymers784,12712
Non-polymers5,04060
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area120690 Å2
ΔGint-807.3 kcal/mol
Surface area274300 Å2
MethodPQS
Unit cell
Length a, b, c (Å)185.948, 185.948, 180.279
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.49805, -0.64468, -0.57994), (-0.64855, -0.167, 0.74262), (-0.57561, 0.74598, -0.33494)84.0302, 106.23995, -45.91362
2given(-0.30535, 0.75914, -0.57487), (0.18082, 0.63894, 0.7477), (0.93491, 0.12436, -0.33237)-66.71606, 19.55266, 20.64046
3given(-0.00168, -0.36045, 0.93278), (-0.93403, 0.33375, 0.12728), (-0.35719, -0.87103, -0.33723)14.70704, 68.26653, 127.67924

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Components

#1: Protein
VANADIUM-DEPENDENT BROMOPEROXIDASE 1 / VANADIUM BROMOPEROXIDASE


Mass: 65343.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORALLINA PILULIFERA (eukaryote) / Plasmid: PTNT30 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BJ1991 / References: UniProt: O81959
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2328 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROLINE 422 HAS BEEN PROVED TO BE ALANINE

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 4 / Details: 0.1M TRIS/H2SO4, 2M NH4H2PO4, pH 4.00
Crystal grow
*PLUS
pH: 3.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris1reservoirpH7.4
2100 mMcitric acid-potassium dihydrogenphosphate1droppH3.8
310 mMEDTA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→22 Å / Num. obs: 178580 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.3 / % possible all: 98

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QHB

1qhb


Resolution: 2.2→22 Å / SU B: 4.82 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.223 8213 5 %RANDOM
Rwork0.168 ---
obs0.17 157072 93 %-
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18420 0 84 2328 20832

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