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- PDB-3n54: Crystal Structure of the GerBC protein -

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Basic information

Entry
Database: PDB / ID: 3n54
TitleCrystal Structure of the GerBC protein
ComponentsSpore germination protein B3Germination
KeywordsLIPID BINDING PROTEIN / a novel fold
Function / homology
Function and homology information


spore germination / plasma membrane
Similarity search - Function
Nutrient germinant receptor protein C, domain 3 / Nuclear Transport Factor 2; Chain: A, / Nutrient germinant receptor protein C, domain 1 / Spore germination GerAC / Spore germination GerAC, C-terminal domain superfamily / Spore germination B3/ GerAC like, C-terminal / Other non-globular / GMP Synthetase; Chain A, domain 3 / Special / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Nutrient germinant receptor protein C, domain 3 / Nuclear Transport Factor 2; Chain: A, / Nutrient germinant receptor protein C, domain 1 / Spore germination GerAC / Spore germination GerAC, C-terminal domain superfamily / Spore germination B3/ GerAC like, C-terminal / Other non-globular / GMP Synthetase; Chain A, domain 3 / Special / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Spore germination protein B3
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLi, Y. / Setlow, B. / Setlow, P. / Hao, B.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of the GerBC Component of a Bacillus subtilis Spore Germinant Receptor.
Authors: Li, Y. / Setlow, B. / Setlow, P. / Hao, B.
History
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Spore germination protein B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,97219
Polymers39,7881
Non-polymers1,18418
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spore germination protein B3
hetero molecules

B: Spore germination protein B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,94338
Polymers79,5762
Non-polymers2,36736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_454y-2/3,x+2/3,-z-1/31
Buried area11920 Å2
ΔGint-381 kcal/mol
Surface area33160 Å2
MethodPISA
3
B: Spore germination protein B3
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)245,830114
Polymers238,7286
Non-polymers7,102108
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation16_454y-2/3,x+2/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area53150 Å2
ΔGint-1352 kcal/mol
Surface area82100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.785, 142.785, 187.827
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-5-

SO4

21B-8-

SO4

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Components

#1: Protein Spore germination protein B3 / Germination


Mass: 39788.031 Da / Num. of mol.: 1 / Fragment: GerBC, residues 25-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU35820, gerBC / Plasmid: a modified pET15b vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39571
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 4.63 Å3/Da / Density % sol: 73.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 1.5-1.7 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2009 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 33056 / Num. obs: 33056 / % possible obs: 99.9 % / Redundancy: 21.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 45.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 21.3 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.338 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.163
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23508 1654 5 %RANDOM
Rwork0.21861 ---
obs0.21944 31175 99.87 %-
all-31175 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.873 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 54 178 2740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222594
X-RAY DIFFRACTIONr_bond_other_d0.0010.021781
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9713497
X-RAY DIFFRACTIONr_angle_other_deg0.77834359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0485307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87324.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80515483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2441512
X-RAY DIFFRACTIONr_chiral_restr0.0530.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
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_it0.5181.51543
X-RAY DIFFRACTIONr_mcbond_other0.0621.5629
X-RAY DIFFRACTIONr_mcangle_it0.97922503
X-RAY DIFFRACTIONr_scbond_it1.08731051
X-RAY DIFFRACTIONr_scangle_it1.8734.5994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 121 -
Rwork0.286 2265 -
obs--99.83 %
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)
110.3609-2.2938-4.6733.6373.176.42390.0338-0.2027-0.1072-0.09150.0757-0.10150.1721-0.0737-0.10950.07960.0116-0.07430.0595-0.00730.0216-84.409524.2647-39.8635
22.2352-1.0351.62141.288-0.4261.8593-0.0239-0.28390.0030.1582-0.0158-0.04590.1522-0.13240.03980.1951-0.02540.03720.09580.04550.0653-73.172621.2654-18.6662
32.99221.2235-0.47927.5125-2.23854.24790.0621-0.3832-0.09490.6601-0.1157-0.1403-0.1105-0.27460.05360.18810.0064-0.01760.1190.12580.04-65.320414.4488-5.6733
43.67760.7534-1.675.5702-3.69884.93140.1697-0.18370.09921.0809-0.8186-1.163-0.56540.79210.64890.2962-0.1492-0.27560.10040.26730.3839-52.299412.65542.4542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B0 - 68
2X-RAY DIFFRACTION2B69 - 146
3X-RAY DIFFRACTION3B147 - 225
4X-RAY DIFFRACTION4B226 - 343

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