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- PDB-1m3s: Crystal structure of YckF from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1m3s
TitleCrystal structure of YckF from Bacillus subtilis
ComponentsHypothetical protein yckf
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


6-phospho-3-hexuloisomerase / hexulose-6-phosphate isomerase activity / formaldehyde assimilation via ribulose monophosphate cycle / carbohydrate derivative metabolic process / carbohydrate derivative binding / response to toxic substance
Similarity search - Function
3-hexulose-6-phosphate isomerase / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hexulose-6-phosphate isomerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsSanishvili, R. / Wu, R. / Kim, D.E. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Crystal structure of Bacillus subtilis YckF: structural and functional evolution.
Authors: Sanishvili, R. / Wu, R. / Kim, D.E. / Watson, J.D. / Collart, F. / Joachimiak, A.
History
DepositionJun 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 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 protein yckf
B: Hypothetical protein yckf


Theoretical massNumber of molelcules
Total (without water)40,0862
Polymers40,0862
Non-polymers00
Water3,657203
1
A: Hypothetical protein yckf
B: Hypothetical protein yckf

A: Hypothetical protein yckf
B: Hypothetical protein yckf


Theoretical massNumber of molelcules
Total (without water)80,1724
Polymers80,1724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area14120 Å2
ΔGint-114 kcal/mol
Surface area26710 Å2
MethodPISA
2
A: Hypothetical protein yckf

B: Hypothetical protein yckf


Theoretical massNumber of molelcules
Total (without water)40,0862
Polymers40,0862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4320 Å2
ΔGint-31 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.080, 72.080, 245.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Hypothetical protein yckf


Mass: 20042.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YckF / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P42404
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Na cacodylate, Ca acetate, Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
214 %PEG80001reservoir
380 mMsodium cacodylate1reservoirpH6.5
4160 mMcalcium acetate1reservoir
520 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9795, 0.9793, 0.9537
SYNCHROTRONAPS 19-ID21.0332
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDMar 17, 2002Sagitally focusing double crystal monochromator and vertically focusing mirror
CUSTOM-MADE2CCDJun 7, 2002Sagitally focusing double crystal monochromator and vertically focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.95371
41.03321
ReflectionResolution: 1.95→60 Å / Num. all: 28687 / Num. obs: 28572 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Rsym value: 0.072 / Net I/σ(I): 31.6
Reflection shellResolution: 1.95→2.01 Å / Mean I/σ(I) obs: 5 / Num. unique all: 2457 / Rsym value: 0.468 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 60 Å

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Processing

Software
NameVersionClassification
REFMAC5refinement
dtDisplaydata collection
HKL-2000data reduction
CNSrefinement
d*TREKdata scaling
d*TREKdata reduction
DTDISPLAYdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→62.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.878 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22493 1389 5.1 %RANDOM
Rwork0.18708 ---
all0.18897 28572 --
obs0.18897 26023 95.85 %-
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: 18.524 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.23 Å20 Å2
2--0.45 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.95→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 0 205 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212861
X-RAY DIFFRACTIONr_bond_other_d0.0030.022646
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9673873
X-RAY DIFFRACTIONr_angle_other_deg1.17636209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14615543
X-RAY DIFFRACTIONr_chiral_restr0.110.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023158
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02504
X-RAY DIFFRACTIONr_nbd_refined0.2440.2600
X-RAY DIFFRACTIONr_nbd_other0.2680.22913
X-RAY DIFFRACTIONr_nbtor_other0.0920.21607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.2132
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.223
X-RAY DIFFRACTIONr_mcbond_it1.1291.51835
X-RAY DIFFRACTIONr_mcangle_it1.87522947
X-RAY DIFFRACTIONr_scbond_it2.94131026
X-RAY DIFFRACTIONr_scangle_it4.4864.5917
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 101
Rwork0.202 1745
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)
12.53110.2270.09721.8310.32022.6660.14830.040.3375-0.1638-0.0291-0.2212-0.35020.1268-0.11920.188-0.03540.08490.00940.00010.133116.191651.815816.3063
23.31240.4034-0.45121.3045-0.17241.67030.14090.2074-0.4953-0.2093-0.03370.010.34630.0926-0.10730.27480.0418-0.04940.0406-0.06010.178413.088418.33648.9573
31.03950.12620.09621.13980.16780.87970.110.0873-0.0222-0.2398-0.0561-0.0435-0.038-0.0066-0.05390.2486-0.00220.02240.20280.00730.23213.807135.71112.5807
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1851 - 186
2X-RAY DIFFRACTION2BB0 - 1851 - 186
3X-RAY DIFFRACTION3A - BA - B186 - 2031 - 279
Refinement
*PLUS
Lowest resolution: 62 Å / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2 Å / Rfactor Rwork: 0.201

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