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- PDB-2fb5: Structural Genomics; The crystal structure of the hypothetical me... -

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Basic information

Entry
Database: PDB / ID: 2fb5
TitleStructural Genomics; The crystal structure of the hypothetical membrane spanning protein from Bacillus cereus
Componentshypothetical Membrane Spanning Protein
KeywordsMEMBRANE PROTEIN / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


diadenylate cyclase / : / cAMP biosynthetic process / adenylate cyclase activity / nucleotidyltransferase activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function
Uncharacterised domain YojJ, N-terminal / Diadenylate cyclase CdaS, N-terminal / Diadenylate cyclase CdaS / YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / YojJ-like / Diadenylate cyclase / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding ...Uncharacterised domain YojJ, N-terminal / Diadenylate cyclase CdaS, N-terminal / Diadenylate cyclase CdaS / YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / YojJ-like / Diadenylate cyclase / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. / Helix Hairpins / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Diadenylate cyclase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsZhang, R. / Zhou, M. / Ginell, S. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the hypothetical membrane spanning protein from Bacillus cereus
Authors: Zhang, R. / Zhou, M. / Ginell, S. / Abdullah, J. / Collart, F. / Joachimiak, A.
History
DepositionDec 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical Membrane Spanning Protein
B: hypothetical Membrane Spanning Protein
C: hypothetical Membrane Spanning Protein


Theoretical massNumber of molelcules
Total (without water)67,7243
Polymers67,7243
Non-polymers00
Water15,241846
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical Membrane Spanning Protein

A: hypothetical Membrane Spanning Protein

B: hypothetical Membrane Spanning Protein

C: hypothetical Membrane Spanning Protein

C: hypothetical Membrane Spanning Protein


Theoretical massNumber of molelcules
Total (without water)112,8745
Polymers112,8745
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation3_544x+1/2,y-1/2,z-11
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area13340 Å2
ΔGint-123 kcal/mol
Surface area55660 Å2
MethodPISA
3
A: hypothetical Membrane Spanning Protein
B: hypothetical Membrane Spanning Protein
C: hypothetical Membrane Spanning Protein

A: hypothetical Membrane Spanning Protein
B: hypothetical Membrane Spanning Protein
C: hypothetical Membrane Spanning Protein


Theoretical massNumber of molelcules
Total (without water)135,4486
Polymers135,4486
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)109.614, 109.609, 77.484
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

21A-395-

HOH

31B-487-

HOH

DetailsThis protein existed as trimer. The molecules A, B, C represent the trimer in the asymmetric unit.

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Components

#1: Protein hypothetical Membrane Spanning Protein


Mass: 22574.748 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: GI:29898520 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 30022961, UniProt: Q812L9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.18M Sodium Malonate, 18% PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.99→77.62 Å / Num. all: 62291 / Num. obs: 61484 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 30.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.51 / Num. unique all: 7786 / % possible all: 73.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.99→77.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.966 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 3111 5.1 %RANDOM
Rwork0.18151 ---
obs0.18325 58372 98.7 %-
all-59141 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.915 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å23.43 Å2
2---2.25 Å20 Å2
3---0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.035 Å0.028 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.029 Å
Refinement stepCycle: LAST / Resolution: 1.99→77.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 0 846 5577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224806
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9676528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6755609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53125.303198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97215864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3761518
X-RAY DIFFRACTIONr_chiral_restr0.080.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023489
X-RAY DIFFRACTIONr_nbd_refined0.2030.22204
X-RAY DIFFRACTIONr_nbtor_refined0.30.23360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2653
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.2142
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.291
X-RAY DIFFRACTIONr_mcbond_it0.7781.53161
X-RAY DIFFRACTIONr_mcangle_it1.30324935
X-RAY DIFFRACTIONr_scbond_it2.10531849
X-RAY DIFFRACTIONr_scangle_it3.4144.51593
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 191 -
Rwork0.201 3886 -
obs--90.54 %
Refinement TLS params.Method: refined / Origin x: 39.419 Å / Origin y: 103.765 Å / Origin z: 27.804 Å
111213212223313233
T-0.0739 Å2-0.0012 Å2-0.0881 Å2-0.032 Å2-0.0008 Å2---0.0311 Å2
L0.0586 °2-0.0085 °2-0.0494 °2-0.1393 °20.0018 °2--0.0931 °2
S0.01 Å °-0.0032 Å °0.0152 Å °0.0027 Å °-0.0113 Å °-0.0078 Å °0.0141 Å °0.0085 Å °0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 802 - 80
2X-RAY DIFFRACTION1AA81 - 15881 - 158
3X-RAY DIFFRACTION1AA161 - 205161 - 205
4X-RAY DIFFRACTION1BB2 - 802 - 80
5X-RAY DIFFRACTION1BB81 - 16081 - 160
6X-RAY DIFFRACTION1BB161 - 205161 - 205
7X-RAY DIFFRACTION1CC2 - 802 - 80
8X-RAY DIFFRACTION1CC81 - 15881 - 158
9X-RAY DIFFRACTION1CC161 - 205161 - 205

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