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- PDB-3oyo: Crystal structure of hemopexin fold protein CP4 from cow pea -

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Basic information

Entry
Database: PDB / ID: 3oyo
TitleCrystal structure of hemopexin fold protein CP4 from cow pea
Componentshemopexin fold protein CP4
KeywordsPLANT PROTEIN / Hemopexin / seeds
Function / homology
Function and homology information


4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Mainly Beta
Similarity search - Domain/homology
Hemopexin fold protein CP4
Similarity search - Component
Biological speciesVigna unguiculata (cowpea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGaur, V. / Chanana, V. / Salunke, D.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: The structure of a haemopexin-fold protein from cow pea (Vigna unguiculata) suggests functional diversity of haemopexins in plants
Authors: Gaur, V. / Chanana, V. / Jain, A. / Salunke, D.M.
History
DepositionSep 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
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 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_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_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_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_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: hemopexin fold protein CP4
B: hemopexin fold protein CP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6788
Polymers49,4812
Non-polymers1976
Water3,279182
1
A: hemopexin fold protein CP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8394
Polymers24,7411
Non-polymers993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hemopexin fold protein CP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8394
Polymers24,7411
Non-polymers993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.087, 60.138, 67.574
Angle α, β, γ (deg.)90.00, 111.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hemopexin fold protein CP4


Mass: 24740.721 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna unguiculata (cowpea) / References: UniProt: F2Z290*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM Tris-HCl, 30% PEG 8000 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 8, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 27508 / % possible obs: 97.4 % / Rmerge(I) obs: 0.105
Reflection shellResolution: 2.1→2.154 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 1.13 / Num. unique all: 490 / % possible all: 95.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LP9

3lp9


Resolution: 2.1→26.22 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.891 / SU B: 5.413 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24648 2517 10 %RANDOM
Rwork0.20481 ---
obs0.20895 22725 91.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.66 Å2
2---0.64 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 6 182 3692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223602
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9544898
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5295448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.52523.78164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55615542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5651516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21732
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22512
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.511.52238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.67823614
X-RAY DIFFRACTIONr_scbond_it1.97931395
X-RAY DIFFRACTIONr_scangle_it2.9924.51284
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 162 -
Rwork0.239 1427 -
obs--78.74 %

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