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- PDB-1vr4: Crystal Structure of MCSG TArget APC22750 from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 1vr4
TitleCrystal Structure of MCSG TArget APC22750 from Bacillus cereus
Componentshypothetical protein APC22750Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pentamer / Hypothetical Protein / PSI / Protein Structure Initiative / The Midwest Center for Structural Genomics / MCSG
Function / homologyUncharacterised protein family UPF0145, YbjQ-like / Putative heavy-metal-binding / UPF0145 domain superfamily / Hypothetical protein apc22750. Chain B / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta / UPF0145 protein BC_1012
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsYang, X. / Brunzelle, J.S. / McNamara, L.K. / Minasov, G. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of MCSG TArget APC22750 from Bacillus cereus
Authors: Brunzelle, J.S. / McNamara, L.K. / Yang, X. / Minasov, G. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. / MCSG
History
DepositionJan 31, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2005ID: 1YBB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein APC22750
B: hypothetical protein APC22750
C: hypothetical protein APC22750
D: hypothetical protein APC22750
E: hypothetical protein APC22750


Theoretical massNumber of molelcules
Total (without water)55,2345
Polymers55,2345
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-51 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.940, 53.560, 53.480
Angle α, β, γ (deg.)65.88, 70.37, 70.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
hypothetical protein APC22750 / Hypothesis


Mass: 11046.733 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q81H14
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 99.8 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 24, 2004 / Details: Mirror
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.09→30 Å / Num. all: 28306 / Num. obs: 26115 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.109 / Net I/σ(I): 12.4
Reflection shellResolution: 2.09→2.18 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.6 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→25 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.861 / SU B: 7.28 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27655 2117 8.6 %RANDOM
Rwork0.21015 ---
all0.21609 26115 --
obs0.21609 22639 87.14 %-
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: 11.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.72 Å2-0.41 Å2
2---0.03 Å2-1.07 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.09→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 0 151 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223586
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9764806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022522
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21755
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.52320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34323737
X-RAY DIFFRACTIONr_scbond_it2.38131266
X-RAY DIFFRACTIONr_scangle_it3.9514.51069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.148 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 80
Rwork0.239 1168
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.05731.0471-0.82254.8667-0.693.0997-0.0940.07-0.23960.03480.09460.15870.2085-0.1787-0.00070.09290.0197-0.0060.0579-0.01970.036114.209629.9515-0.8951
28.8699-1.6-1.96084.78580.33784.81990.0116-0.3411-0.31160.3563-0.0420.0090.0927-0.08450.03040.0917-0.0019-0.02710.0001-0.00160.050117.491725.459611.7104
37.2324-3.686-1.18634.45210.79162.9529-0.0071-0.3754-0.05470.46630.06720.07790.1236-0.162-0.06010.1659-0.05290.01830.09680.01270.051713.285439.140123.8983
47.0662-1.03872.99952.5389-0.2174.2295-0.10650.02810.2805-0.0528-0.05010.2713-0.3623-0.22790.15660.08250.02130.00210.0258-0.00350.08412.411953.730414.19
52.90322.75581.36194.72161.92593.1805-0.1640.18620.0398-0.1630.08650.1059-0.0734-0.20550.07760.07570.00830.01150.07520.03030.039416.268747.1956-2.1929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1031 - 103
2X-RAY DIFFRACTION2BB1 - 1031 - 103
3X-RAY DIFFRACTION3CC1 - 1031 - 103
4X-RAY DIFFRACTION4DD1 - 1031 - 103
5X-RAY DIFFRACTION5EE1 - 1031 - 103

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