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- PDB-3gby: Crystal structure of a protein with unknown function CT1051 from ... -

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Basic information

Entry
Database: PDB / ID: 3gby
TitleCrystal structure of a protein with unknown function CT1051 from Chlorobium tepidum
ComponentsUncharacterized protein CT1051
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Chlorobium tepidum / CBS domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyCBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / Roll / Alpha Beta / CBS domain-containing protein
Function and homology information
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsFan, Y. / Chang, C. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a protein with unknown function CT1051 from Chlorobium tepidum
Authors: Fan, Y. / Chang, C. / Sather, A. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 20, 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 6, 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 CT1051
B: Uncharacterized protein CT1051
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5886
Polymers27,9192
Non-polymers6694
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-21.1 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.045, 38.784, 60.932
Angle α, β, γ (deg.)90.00, 95.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein CT1051


Mass: 13959.722 Da / Num. of mol.: 2 / Fragment: UNP residues 2-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Strain: TLS / DSM 12025 / Gene: CT1051 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8KDJ9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Lithium sulfate, 0.1M HEPES, 25% w/v PEG 3350, pH 7.5, 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: 0.97937 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Feb 6, 2009
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 27829 / Num. obs: 27379 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 43.8
Reflection shellResolution: 1.66→1.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 1.9 / Num. unique all: 425 / % possible all: 59.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.967 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22632 1357 5 %RANDOM
Rwork0.17929 ---
all0.1818 26597 --
obs0.1818 26597 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.659 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å2-0.76 Å2
2--1.02 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 40 249 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5452.0032825
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4135270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48822.18487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55415341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5061523
X-RAY DIFFRACTIONr_chiral_restr0.090.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211559
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2441.51299
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.04922082
X-RAY DIFFRACTIONr_scbond_it3.1763777
X-RAY DIFFRACTIONr_scangle_it4.8734.5740
X-RAY DIFFRACTIONr_rigid_bond_restr1.85832076
X-RAY DIFFRACTIONr_sphericity_free5.7723249
X-RAY DIFFRACTIONr_sphericity_bonded2.62432035
LS refinement shellResolution: 1.66→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 81 -
Rwork0.275 1632 -
obs-1713 84.93 %
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)
12.2306-0.17480.51670.7004-0.51692.28690.02310.1088-0.0018-0.01170.04420.08280.0192-0.0794-0.06730.152400.02020.11280.00480.018422.4249.7294.145
23.61140.69840.52961.48390.35211.70750.07440.1485-0.04930.00760.0211-0.18570.02950.2969-0.09550.15510.02350.02920.2013-0.0240.037543.4255.2946.34
31.91110.4125-0.82721.2277-0.08232.4235-0.0056-0.14660.01580.03430.04480.1078-0.0014-0.0818-0.03930.13830.01250.02750.16410.00660.016920.3389.07325.96
42.2182-1.5283-2.60192.49742.97075.8063-0.0544-0.82060.23410.13550.6515-0.42860.1731.4006-0.59710.14830.0123-0.00390.5518-0.15690.093741.15313.10827.969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 12
2X-RAY DIFFRACTION1A76 - 125
3X-RAY DIFFRACTION2A13 - 75
4X-RAY DIFFRACTION3B-1 - 12
5X-RAY DIFFRACTION3B76 - 125
6X-RAY DIFFRACTION4B13 - 75

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