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- PDB-3d0j: Crystal structure of conserved protein of unknown function CA_C34... -

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Basic information

Entry
Database: PDB / ID: 3d0j
TitleCrystal structure of conserved protein of unknown function CA_C3497 from Clostridium acetobutylicum ATCC 824
ComponentsUncharacterized protein CA_C3497
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-barrel / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyJelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / FORMIC ACID / Cupin
Function and homology information
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 Å
AuthorsKim, Y. / Bigelow, L. / Clancy, S. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Conserved Protein of Unknown Function CA_C3497 from Clostridium acetobutylicum ATCC 824.
Authors: Kim, Y. / Bigelow, L. / Clancy, S. / Abdullah, J. / Joachimiak, A.
History
DepositionMay 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Uncharacterized protein CA_C3497
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9156
Polymers16,6391
Non-polymers2765
Water3,369187
1
A: Uncharacterized protein CA_C3497
hetero molecules

A: Uncharacterized protein CA_C3497
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,83112
Polymers33,2782
Non-polymers55210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area3610 Å2
ΔGint-25.6 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.878, 52.878, 112.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

21A-295-

HOH

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Components

#1: Protein Uncharacterized protein CA_C3497


Mass: 16639.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-term 6-His-tag with TEV protease cleavage site
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 / Gene: CA_C3497 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97DI0
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.5M Sodium formate, 0.1M Sodium acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2008 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.53→45.79 Å / Num. all: 27647 / Num. obs: 27647 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 19.19 Å2 / Rsym value: 0.086 / Net I/σ(I): 12.1
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1343 / Rsym value: 0.691 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.53→45.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.244 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.068
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1421 5 %RANDOM
Rwork0.165 ---
all0.166 26887 --
obs0.166 26887 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.53→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 18 187 1338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.9661867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23426.61868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25815277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.092153
X-RAY DIFFRACTIONr_chiral_restr0.1260.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021074
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.2580
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2950
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2381.5868
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76221353
X-RAY DIFFRACTIONr_scbond_it2.6623595
X-RAY DIFFRACTIONr_scangle_it4.0894.5514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 102 -
Rwork0.229 1904 -
obs-2006 100 %
Refinement TLS params.Method: refined / Origin x: 30.8807 Å / Origin y: 0.0452 Å / Origin z: 5.3395 Å
111213212223313233
T-0.0078 Å2-0.0264 Å20.0073 Å2--0.0504 Å2-0.0066 Å2---0.0231 Å2
L0.1861 °20.0323 °20.0981 °2-0.2222 °20.1914 °2--1.0179 °2
S-0.0542 Å °0.0312 Å °-0.0046 Å °-0.0389 Å °0.0707 Å °0.0051 Å °-0.0538 Å °0.0636 Å °-0.0165 Å °

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