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- PDB-2hq8: Crystal structure of coelenterazine-binding protein from renilla ... -

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Basic information

Entry
Database: PDB / ID: 2hq8
TitleCrystal structure of coelenterazine-binding protein from renilla muelleri in the ca loaded apo form
ComponentsCoelenterazine-binding protein ca-bound apo form
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / COELENTERAZINE-BINDING PROTEIN / RENILLA MUELLERI / PSI / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / Protein Structure Initiative / SECSG
Function / homology
Function and homology information


bioluminescence / calcium ion binding
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Luciferin-binding protein
Similarity search - Component
Biological speciesRenilla muelleri (Mueller's sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / S,CA-SAS / Resolution: 1.8 Å
AuthorsStepanyuk, G. / Liu, Z.J. / Vysotski, E.S. / Lee, J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: PHOTOCHEM.PHOTOBIOL.SCI. / Year: 2008
Title: Crystal structure of coelenterazine-binding protein from Renilla muelleri at 1.7 A: why it is not a calcium-regulated photoprotein.
Authors: Stepanyuk, G.A. / Liu, Z.J. / Markova, S.S. / Frank, L.A. / Lee, J. / Vysotski, E.S. / Wang, B.C.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE A suitable database reference was not available at the time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coelenterazine-binding protein ca-bound apo form
B: Coelenterazine-binding protein ca-bound apo form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9468
Polymers41,7052
Non-polymers2406
Water5,405300
1
A: Coelenterazine-binding protein ca-bound apo form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9734
Polymers20,8531
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coelenterazine-binding protein ca-bound apo form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9734
Polymers20,8531
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.414, 78.414, 125.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Coelenterazine-binding protein ca-bound apo form


Mass: 20852.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Renilla muelleri (Mueller's sea pansy) / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P05938
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROP VAPOR DIFFUSION USING 0.5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (13.5 MG/ML) AND RESERVOIR SOLUTION CONTAING 2% PEG 4000, 2.0M AMMONIUM SULFATE, 0.1M ...Details: SITTING DROP VAPOR DIFFUSION USING 0.5 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (13.5 MG/ML) AND RESERVOIR SOLUTION CONTAING 2% PEG 4000, 2.0M AMMONIUM SULFATE, 0.1M HEPES PH 7.5, VAPOR DIFFUSION, temperature 291K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2005 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 39679 / Num. obs: 37300 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rsym value: 0.042 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Num. unique all: 3425 / Rsym value: 0.32 / % possible all: 84.4

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Processing

Software
NameVersionClassification
SCA2STRUCTUREmodel building
REFMAC5.2.0005refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SCA2STRUCTUREphasing
RefinementMethod to determine structure: S,CA-SAS / Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.782 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24747 2079 5.3 %RANDOM
Rwork0.20473 ---
all0.20697 37300 --
obs0.20697 37300 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.749 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 6 300 3104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222836
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9683830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5635361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31124.776134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34815498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4561519
X-RAY DIFFRACTIONr_chiral_restr0.1160.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022123
X-RAY DIFFRACTIONr_nbd_refined0.2280.21509
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2231
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0790.210
X-RAY DIFFRACTIONr_mcbond_it0.9881.51848
X-RAY DIFFRACTIONr_mcangle_it1.57222885
X-RAY DIFFRACTIONr_scbond_it2.83231094
X-RAY DIFFRACTIONr_scangle_it4.2584.5945
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 126 -
Rwork0.299 2175 -
obs--84.4 %

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