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- PDB-4jgi: 1.5 Angstrom crystal structure of a novel cobalamin-binding prote... -

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Basic information

Entry
Database: PDB / ID: 4jgi
Title1.5 Angstrom crystal structure of a novel cobalamin-binding protein from Desulfitobacterium hafniense DCB-2
ComponentsPutative uncharacterized protein
KeywordsPROTEIN BINDING / Rossmann fold / cobalamin binding / cobalamin
Function / homology
Function and homology information


cobalamin binding / metal ion binding
Similarity search - Function
Methionine synthase domain / B12-binding N-terminal domain profile. / B12 binding domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily ...Methionine synthase domain / B12-binding N-terminal domain profile. / B12 binding domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / Uncharacterized protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSjuts, H. / Dunstan, M.S. / Fisher, K. / Leys, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the cobalamin-binding protein of a putative O-demethylase from Desulfitobacterium hafniense DCB-2.
Authors: Sjuts, H. / Dunstan, M.S. / Fisher, K. / Leys, D.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 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_ref_seq_dif / 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_label_asym_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_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8044
Polymers45,1162
Non-polymers2,6892
Water7,584421
1
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9022
Polymers22,5581
Non-polymers1,3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9022
Polymers22,5581
Non-polymers1,3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Putative uncharacterized protein
hetero molecules

B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8044
Polymers45,1162
Non-polymers2,6892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z+1/31
Buried area4620 Å2
ΔGint-35 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.990, 69.990, 91.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Putative uncharacterized protein


Mass: 22557.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q8RPG0
#2: Chemical ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H91CoN13O14P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M MMT buffer, 25 % w/v PEG 1500, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.95 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2012
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.5→32.7 Å / Num. all: 78874 / Num. obs: 75677 / % possible obs: 99 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
xia2XDSdata reduction
xia2XDS scaledata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→32.69 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.603 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 3997 5 %RANDOM
Rwork0.14728 ---
obs0.14971 75677 99.05 %-
all-78874 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å2-0 Å2
2--0.03 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 182 421 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193295
X-RAY DIFFRACTIONr_bond_other_d0.0010.0193235
X-RAY DIFFRACTIONr_angle_refined_deg2.141.9984484
X-RAY DIFFRACTIONr_angle_other_deg1.01837418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28726.269134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48515555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3451514
X-RAY DIFFRACTIONr_chiral_restr0.140.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02669
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr7.08836530
X-RAY DIFFRACTIONr_sphericity_free22.1385102
X-RAY DIFFRACTIONr_sphericity_bonded12.05356801
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 314 -
Rwork0.224 5479 -
obs--97.38 %

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