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- PDB-2rbd: CRYSTAL STRUCTURE OF A PUTATIVE SPORE COAT PROTEIN (BH2358) FROM ... -

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Basic information

Entry
Database: PDB / ID: 2rbd
TitleCRYSTAL STRUCTURE OF A PUTATIVE SPORE COAT PROTEIN (BH2358) FROM BACILLUS HALODURANS C-125 AT 1.54 A RESOLUTION
ComponentsBH2358 protein
KeywordsSTRUCTURAL PROTEIN / PUTATIVE SPORE COAT PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyProtein of unknown function DUF3231 / Protein of unknown function (DUF3231) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Up-down Bundle / Mainly Alpha / BH2358 protein
Function and homology information
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a domain with unknown function and a ferritin-like fold (NP_243224.1) from Bacillus halodurans at 1.54 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH2358 protein
B: BH2358 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9705
Polymers38,3882
Non-polymers5833
Water7,728429
1
A: BH2358 protein
B: BH2358 protein
hetero molecules

A: BH2358 protein
B: BH2358 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,94010
Polymers76,7754
Non-polymers1,1656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y+1/2,z1
Buried area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.082, 74.345, 235.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-172-

PG4

21A-172-

PG4

31A-216-

HOH

41A-284-

HOH

51A-305-

HOH

61B-237-

HOH

71B-272-

HOH

81B-312-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 10 - 164 / Label seq-ID: 11 - 165

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein BH2358 protein


Mass: 19193.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: NP_243224.1, BH2358 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KAD1
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: NANODROP, 0.2M Li3 Citrate, 20.0% PEG 3350, No Buffer pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97898, 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 26, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978981
30.979221
ReflectionResolution: 1.54→39.809 Å / Num. obs: 56674 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.54-1.626.10.681.14967081620.6899.9
1.62-1.726.10.5221.54720077570.52299.9
1.72-1.846.10.3532.24438772570.353100
1.84-1.996.10.2243.44151767890.224100
1.99-2.186.10.1216.33840662760.121100
2.18-2.436.10.0839.23487957010.083100
2.43-2.816.10.05812.83088650590.05899.9
2.81-3.446.10.03818.22615943150.038100
3.44-4.875.90.02426.92015133900.024100
4.87-39.8095.50.02523.11081319680.02599.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.54→39.809 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.562 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.80 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. PG4 (PEG 200) MOLECULES FROM THE CRYSTALLIZATION SOLUTION WERE MODELED. PG4 3 IS LOCATED ON 2-FOLD AXIS, IT COULD BE A NOISE. 4. RESIDUES A0-6, B0-9, A/B166-170 ARE DISORDERED AND NOT MODELED. DENSITIES NEAR A20 AND B20, N-TERMINUS, C-TERMINUS WERE LEFT UNINTERPRETED.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2882 5.1 %RANDOM
Rwork0.159 ---
obs0.16 56673 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.54→39.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 39 429 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222747
X-RAY DIFFRACTIONr_bond_other_d0.0010.021879
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9723783
X-RAY DIFFRACTIONr_angle_other_deg0.95434671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7545393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.29325.581129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70515469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3841512
X-RAY DIFFRACTIONr_chiral_restr0.090.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
X-RAY DIFFRACTIONr_nbd_refined0.2210.2660
X-RAY DIFFRACTIONr_nbd_other0.1830.21934
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21355
X-RAY DIFFRACTIONr_nbtor_other0.0910.21407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2306
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.247
X-RAY DIFFRACTIONr_mcbond_it2.25131831
X-RAY DIFFRACTIONr_mcbond_other0.6123670
X-RAY DIFFRACTIONr_mcangle_it2.86652787
X-RAY DIFFRACTIONr_scbond_it4.81981124
X-RAY DIFFRACTIONr_scangle_it7.04611955
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1936 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.360.5
MEDIUM THERMAL1.242
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 206 -
Rwork0.268 3908 -
all-4114 -
obs--100 %

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