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- PDB-3g7g: Crystal structure of the protein with unknown function from Clost... -

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Basic information

Entry
Database: PDB / ID: 3g7g
TitleCrystal structure of the protein with unknown function from Clostridium acetobutylicum ATCC 824
ComponentsUPF0311 protein CA_C3321
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein with unknown fuction / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyUncharacterised protein family UPF0311 / Protein of unknown function (DUF3237) / Porin - #20 / Porin / Beta Barrel / Mainly Beta / UPF0311 protein CA_C3321
Function and homology information
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsZhang, R. / Wu, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein with unknown function from Clostridium acetobutylicum ATCC 824
Authors: Zhang, R. / Wu, R. / Abdullah, J. / Joachimiak, A.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0311 protein CA_C3321
B: UPF0311 protein CA_C3321
D: UPF0311 protein CA_C3321
E: UPF0311 protein CA_C3321
C: UPF0311 protein CA_C3321
F: UPF0311 protein CA_C3321
G: UPF0311 protein CA_C3321
H: UPF0311 protein CA_C3321


Theoretical massNumber of molelcules
Total (without water)143,5338
Polymers143,5338
Non-polymers00
Water9,116506
1
A: UPF0311 protein CA_C3321
B: UPF0311 protein CA_C3321
D: UPF0311 protein CA_C3321
E: UPF0311 protein CA_C3321


Theoretical massNumber of molelcules
Total (without water)71,7664
Polymers71,7664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-47.1 kcal/mol
Surface area25440 Å2
MethodPISA
2
C: UPF0311 protein CA_C3321
F: UPF0311 protein CA_C3321
G: UPF0311 protein CA_C3321
H: UPF0311 protein CA_C3321


Theoretical massNumber of molelcules
Total (without water)71,7664
Polymers71,7664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-46.8 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.048, 166.841, 66.974
Angle α, β, γ (deg.)90.00, 119.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
UPF0311 protein CA_C3321


Mass: 17941.586 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum ATCC 824 (bacteria)
Strain: DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 / Gene: CA_C3321 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q97DZ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1M Bis-tris, 0.2M NaCl, pH 6.5, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2007 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.99→58.62 Å / Num. all: 82931 / Num. obs: 81173 / % possible obs: 97.88 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 12.63
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.47 / Num. unique all: 6459 / % possible all: 84.82

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.99→58.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.173 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.181
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 4251 5 %RANDOM
Rwork0.19344 ---
all0.19649 81173 --
obs0.19649 81173 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.322 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å22.04 Å2
2---1.89 Å20 Å2
3---1.85 Å2
Refinement stepCycle: LAST / Resolution: 1.99→58.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9298 0 0 506 9804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229542
X-RAY DIFFRACTIONr_bond_other_d0.0020.026618
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.96812908
X-RAY DIFFRACTIONr_angle_other_deg0.966316114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97151156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92923.871434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.819151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7011564
X-RAY DIFFRACTIONr_chiral_restr0.1050.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021941
X-RAY DIFFRACTIONr_nbd_refined0.2110.21549
X-RAY DIFFRACTIONr_nbd_other0.2110.27019
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24528
X-RAY DIFFRACTIONr_nbtor_other0.090.25497
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2480
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.217
X-RAY DIFFRACTIONr_mcbond_it1.4831.57474
X-RAY DIFFRACTIONr_mcbond_other0.4081.52355
X-RAY DIFFRACTIONr_mcangle_it1.83629500
X-RAY DIFFRACTIONr_scbond_it3.10734377
X-RAY DIFFRACTIONr_scangle_it4.3014.53408
LS refinement shellResolution: 1.99→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 276 -
Rwork0.216 5168 -
obs-5444 84.82 %
Refinement TLS params.Method: refined / Origin x: 35.94 Å / Origin y: 48.995 Å / Origin z: -33.084 Å
111213212223313233
T-0.0413 Å20.0055 Å2-0.0217 Å2--0.0556 Å2-0.004 Å2---0.0329 Å2
L0.0127 °20.0402 °2-0.0428 °2-0.466 °2-0.1953 °2--0.1822 °2
S0.0137 Å °-0.0103 Å °0.0014 Å °-0.0131 Å °-0.0084 Å °0.023 Å °0.0019 Å °0.0215 Å °-0.0053 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 50
2X-RAY DIFFRACTION1A51 - 98
3X-RAY DIFFRACTION1A100 - 158
4X-RAY DIFFRACTION1B9 - 50
5X-RAY DIFFRACTION1B51 - 106
6X-RAY DIFFRACTION1B113 - 158
7X-RAY DIFFRACTION1D8 - 50
8X-RAY DIFFRACTION1D51 - 108
9X-RAY DIFFRACTION1D113 - 158
10X-RAY DIFFRACTION1E8 - 50
11X-RAY DIFFRACTION1E51 - 98
12X-RAY DIFFRACTION1E113 - 158
13X-RAY DIFFRACTION1C9 - 50
14X-RAY DIFFRACTION1C51 - 108
15X-RAY DIFFRACTION1C114 - 158
16X-RAY DIFFRACTION1F6 - 50
17X-RAY DIFFRACTION1F51 - 108
18X-RAY DIFFRACTION1F111 - 158
19X-RAY DIFFRACTION1G9 - 50
20X-RAY DIFFRACTION1G51 - 108
21X-RAY DIFFRACTION1G113 - 158
22X-RAY DIFFRACTION1H5 - 50
23X-RAY DIFFRACTION1H51 - 108
24X-RAY DIFFRACTION1H111 - 158

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