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- PDB-3d19: Crystal structure of a conserved metalloprotein from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 3d19
TitleCrystal structure of a conserved metalloprotein from Bacillus cereus
ComponentsConserved metalloprotein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homologyProtein of unknown function DUF2935 / Ferritin / Up-down Bundle / Mainly Alpha / : / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsBonanno, J.B. / Patskovsky, Y. / Freeman, J. / Bain, K.T. / Chang, S. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. ...Bonanno, J.B. / Patskovsky, Y. / Freeman, J. / Bain, K.T. / Chang, S. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a conserved metalloprotein from Bacillus cereus.
Authors: Bonanno, J.B. / Patskovsky, Y. / Freeman, J. / Bain, K.T. / Chang, S. / Ozyurt, S. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved metalloprotein
B: Conserved metalloprotein
C: Conserved metalloprotein
D: Conserved metalloprotein
E: Conserved metalloprotein
F: Conserved metalloprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,51518
Polymers200,0346
Non-polymers48112
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-124.7 kcal/mol
Surface area56720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.825, 136.378, 87.060
Angle α, β, γ (deg.)90.000, 102.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Conserved metalloprotein


Mass: 33338.992 Da / Num. of mol.: 6 / Fragment: Residues 11-282 / Mutation: L39F, M137I, E138Q, A193E, V211A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: G9241 / Gene: BCE_G9241_1042 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4MW04
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8
Details: 100mM Tris-HCl pH 8.0, 30% PEG 3350, 200mM Magnesium chloride, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.3→47.036 Å / Num. all: 75161 / Num. obs: 75161 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.7 / Num. unique all: 10812 / Rsym value: 0.444 / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.354 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.407 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Unknown metals have been modeled as Fe and Mg due to metalloprotein XAS screening results, observed anomalous Fourier peaks, and presence of Mg in crystallization condition.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3755 5 %RANDOM
Rwork0.206 ---
obs0.21 74793 99.23 %-
all-74793 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.453 Å2
Baniso -1Baniso -2Baniso -3
1-4.56 Å20 Å22.13 Å2
2---2.02 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12908 0 12 129 13049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02213260
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9517894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46951568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63923.824727
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.844152436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.17315114
X-RAY DIFFRACTIONr_chiral_restr0.0990.21948
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110134
X-RAY DIFFRACTIONr_mcbond_it0.7631.57819
X-RAY DIFFRACTIONr_mcangle_it1.491212649
X-RAY DIFFRACTIONr_scbond_it2.65535441
X-RAY DIFFRACTIONr_scangle_it4.244.55237
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 260 -
Rwork0.261 5051 -
all-5311 -
obs-5051 96.16 %

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