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- PDB-4o8w: Crystal Structure of the GerD spore germination protein -

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Basic information

Entry
Database: PDB / ID: 4o8w
TitleCrystal Structure of the GerD spore germination protein
ComponentsSpore germination protein
Keywordsstructural protein / signaling protein / superhelical rope fold / scaffold / spore inner membrane
Function / homologySpore germination GerD, central core domain / Spore germination GerD central core domain / Spore germination protein
Function and homology information
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.293 Å
AuthorsLi, Y. / Jin, K. / Ghosh, S. / Devarakonda, P. / Carlson, K. / Davis, A. / Stewart, K. / Cammett, E. / Rossi, P.P. / Setlow, B. ...Li, Y. / Jin, K. / Ghosh, S. / Devarakonda, P. / Carlson, K. / Davis, A. / Stewart, K. / Cammett, E. / Rossi, P.P. / Setlow, B. / Lu, M. / Setlow, P. / Hao, B.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural and Functional Analysis of the GerD Spore Germination Protein of Bacillus Species.
Authors: Li, Y. / Jin, K. / Ghosh, S. / Devarakonda, P. / Carlson, K. / Davis, A. / Stewart, K.A. / Cammett, E. / Rossi, P.P. / Setlow, B. / Lu, M. / Setlow, P. / Hao, B.
History
DepositionDec 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Feb 28, 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

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Assembly

Deposited unit
A: Spore germination protein
B: Spore germination protein
C: Spore germination protein
D: Spore germination protein
E: Spore germination protein
F: Spore germination protein


Theoretical massNumber of molelcules
Total (without water)86,6216
Polymers86,6216
Non-polymers00
Water2,864159
1
A: Spore germination protein
B: Spore germination protein
C: Spore germination protein


Theoretical massNumber of molelcules
Total (without water)43,3113
Polymers43,3113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint-134 kcal/mol
Surface area17590 Å2
MethodPISA
2
D: Spore germination protein
E: Spore germination protein
F: Spore germination protein


Theoretical massNumber of molelcules
Total (without water)43,3113
Polymers43,3113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-149 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.748, 98.450, 127.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22D
13C
23E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A25 - 122
2116F25 - 122
1126B26 - 122
2126D26 - 122
1136C13 - 120
2136E13 - 120

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Spore germination protein


Mass: 14436.869 Da / Num. of mol.: 6 / Mutation: K113R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: PS3001 / Gene: gerD, GK0144 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5L3Q1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 15% ethyl alcohol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2009 / Details: mirrors
RadiationMonochromator: Yale mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.29→54.47 Å / Num. all: 34394 / Num. obs: 34360 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 39.4 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 30.5
Reflection shellResolution: 2.29→2.38 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 6.3 / Num. unique all: 3365 / Rsym value: 0.463 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.293→54.47 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 15.222 / SU ML: 0.17 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 1 / ESU R: 0.329 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25594 1734 5.1 %RANDOM
Rwork0.20009 ---
all0.21 34938 --
obs0.20283 32570 99.52 %-
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: 64.439 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å20 Å20 Å2
2---4.33 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.293→54.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5193 0 0 159 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225335
X-RAY DIFFRACTIONr_bond_other_d0.0010.023576
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9777188
X-RAY DIFFRACTIONr_angle_other_deg0.8738851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6425698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91326.089202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.915151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6351513
X-RAY DIFFRACTIONr_chiral_restr0.0620.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02943
X-RAY DIFFRACTIONr_mcbond_it1.41833498
X-RAY DIFFRACTIONr_mcbond_other0.35831376
X-RAY DIFFRACTIONr_mcangle_it2.54455545
X-RAY DIFFRACTIONr_scbond_it4.90581837
X-RAY DIFFRACTIONr_scangle_it7.189111643
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1223LOOSE POSITIONAL0.55
1A1223LOOSE THERMAL3.3510
2B1133LOOSE POSITIONAL0.465
2B1133LOOSE THERMAL3.1910
3C1351LOOSE POSITIONAL0.635
3C1351LOOSE THERMAL3.0710
LS refinement shellResolution: 2.293→2.352 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 124 -
Rwork0.188 2240 -
obs-2066 94.79 %
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)
10.8026-0.29840.11460.6522-0.21615.12330.0686-0.07190.22250.05610.0206-0.0362-0.5786-0.2695-0.08920.08230.01750.0390.0316-0.01790.1179-27.6583-3.17727.5145
20.9095-0.34490.01170.472-0.1715.78620.0616-0.06120.20370.0474-0.01050.0021-0.5346-0.1593-0.05110.06890.00020.050.0155-0.03330.1244-27.0667-2.456729.3851
30.8935-0.44540.37690.5773-0.13684.88370.0269-0.04360.21380.0280.0272-0.058-0.5673-0.3275-0.0540.08770.02480.05490.0389-0.03170.1745-27.2988-2.302626.9671
40.32390.0254-1.24540.37520.30396.6420.0225-0.0039-0.04070.08460.0123-0.04850.14570.2191-0.03480.03680.0071-0.00970.0934-0.02860.0904-16.2916-25.96512.6729
50.1947-0.0641-0.44360.11280.27992.70490.0563-0.0163-0.02520.01970.03050.02160.20720.1731-0.08680.08320.0148-0.0140.1181-0.020.111-16.4078-26.2954.9699
60.4065-0.201-0.99950.36571.17646.7427-0.02280.0487-0.06840.062-0.0550.01270.3154-0.05090.07780.0221-0.01280.00620.0497-0.01440.08-17.1264-25.67664.0309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A69 - 178
2X-RAY DIFFRACTION2B63 - 178
3X-RAY DIFFRACTION3C64 - 176
4X-RAY DIFFRACTION4D60 - 179
5X-RAY DIFFRACTION5E61 - 175
6X-RAY DIFFRACTION6F66 - 180

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