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- PDB-1qhb: VANADIUM BROMOPEROXIDASE FROM RED ALGA CORALLINA OFFICINALIS -

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Basic information

Entry
Database: PDB / ID: 1qhb
TitleVANADIUM BROMOPEROXIDASE FROM RED ALGA CORALLINA OFFICINALIS
ComponentsHALOPEROXIDASE
KeywordsOXIDOREDUCTASE / RED ALGA / HALOGENATION / VANADIUM-DEPENDENT
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 / Phosphatidic acid phosphatase type 2/haloperoxidase / Bromoperoxidase/chloroperoxidase C-terminal / PAP2 superfamily / 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 officinalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsIsupov, M.N. / Dalby, A.R. / Brindley, A.A. / Littlechild, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of dodecameric vanadium-dependent bromoperoxidase from the red algae Corallina officinalis.
Authors: Isupov, M.N. / Dalby, A.R. / Brindley, A.A. / Izumi, Y. / Tanabe, T. / Murshudov, G.N. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Preliminary X-Ray Analysis of a New Crystal Form of the Vanadium-Dependent Bromoperoxidase from Corallina officinalis
Authors: Brindley, A.A. / Dalby, A.R. / Isupov, M.N. / Littlechild, J.A.
History
DepositionMay 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 5, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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_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: HALOPEROXIDASE
B: HALOPEROXIDASE
C: HALOPEROXIDASE
D: HALOPEROXIDASE
E: HALOPEROXIDASE
F: HALOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,72718
Polymers388,9166
Non-polymers81012
Water39,3812186
1
A: HALOPEROXIDASE
B: HALOPEROXIDASE
C: HALOPEROXIDASE
D: HALOPEROXIDASE
E: HALOPEROXIDASE
F: HALOPEROXIDASE
hetero molecules

A: HALOPEROXIDASE
B: HALOPEROXIDASE
C: HALOPEROXIDASE
D: HALOPEROXIDASE
E: HALOPEROXIDASE
F: HALOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)779,45336
Polymers777,83312
Non-polymers1,62124
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area105910 Å2
ΔGint-684 kcal/mol
Surface area206430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)201.915, 201.915, 178.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11D-3011-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.51551, -0.48308, 0.70774), (0.50445, -0.49656, -0.70637), (0.69266, 0.72116, -0.01229)-31.66092, 132.4545, 43.53284
2given(0.5185, 0.49229, 0.69915), (-0.48588, -0.50318, 0.71465), (0.70361, -0.71025, -0.02171)-80.5313, 19.62524, 116.74713
3given(-0.99973, 0.00331, 0.02283), (-0.00278, -0.99973, 0.023), (0.0229, 0.02293, 0.99947)-102.08086, 99.88497, -0.00393
4given(-0.49248, 0.50717, -0.70727), (-0.48116, 0.51851, 0.70685), (0.72522, 0.68842, -0.01132)-69.40148, -31.37383, 46.76636
5given(-0.49525, -0.51259, -0.70141), (0.51151, 0.48054, -0.71234), (0.7022, -0.71157, 0.02421)-18.30801, 83.49847, 114.71655

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Components

#1: Protein
HALOPEROXIDASE /


Mass: 64819.402 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Corallina officinalis (eukaryote) / References: UniProt: Q8LLW7, chloride peroxidase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS NO SEQUENCE INFORMATION AVAILABLE FOR CORALLINA OFFICINALIS VANADIUM BROMOPEROXIDASE. ...THERE IS NO SEQUENCE INFORMATION AVAILABLE FOR CORALLINA OFFICINALIS VANADIUM BROMOPEROXIDASE. SEQUENCES OF THE VANADIUM-DEPENDENT BROMOPEROXIDASES 1 AND 2 FROM THE RELATED ORGANISM CORALLINA PILULIFERA WERE USED FOR MODEL BUILDING (GENBANK ACCESSSION CODES BAA31261 AND BAA31262). HOWEVER THE SEQUENCE WAS CHANGED WHERE THE ELECTRON DENSITY SUGGESTED SO. THE RESULTING SEQUENCE SO. THE RESULTING SEQUENCE OF THE CORALLINA OFFICINALIS ENZYME HAS 95 % IDENTITY TO VANADIUM-DEPENDENT BROMOPEROXIDASE 2 FROM CORALLINA PILULIFERA AND 91 % IDENTITY TO BROMOPEROXIDASE 1.

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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: 2.36 Å3/Da / Density % sol: 47.6 %
Crystal growpH: 5
Details: 2M DIHYDROGEN PHOSPHATE, 0.1 M TRIS-HCL BUFFER, FINAL PH 5.
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
22 Mammonium dihydrogen phosphate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 491505 / % possible obs: 96.8 % / Redundancy: 4 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 6.6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.3 / % possible all: 95.2
Reflection
*PLUS
Num. obs: 156862 / Num. measured all: 491505 / Biso Wilson estimate: 21.5 Å2
Reflection shell
*PLUS
% possible obs: 95.2 %

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Processing

Software
NameVersionClassification
SHELXmodel building
MLPHAREphasing
DMmodel building
REFMACWITH INPUT DM PHASESrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→20 Å / SU B: 6.3 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3148 2 %RANDOM
Rwork0.172 ---
obs-153678 94.8 %-
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.194 Å20 Å20 Å2
2--0.194 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27402 0 36 2186 29624
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1654
X-RAY DIFFRACTIONp_mcangle_it2.8636
X-RAY DIFFRACTIONp_scbond_it5.6028
X-RAY DIFFRACTIONp_scangle_it6.87810
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.1160.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1610.3
X-RAY DIFFRACTIONp_planar_tor3.47
X-RAY DIFFRACTIONp_staggered_tor1415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.120
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.4 Å2
Refine LS restraints
*PLUS
Type: p_plane_restr / Dev ideal: 0.021 / Dev ideal target: 0.025

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