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- PDB-4ilq: 2.60A resolution structure of CT771 from Chlamydia trachomatis -

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Basic information

Entry
Database: PDB / ID: 4ilq
Title2.60A resolution structure of CT771 from Chlamydia trachomatis
ComponentsCT771
KeywordsHYDROLASE / hypothetical protein / structural proteomics
Function / homology
Function and homology information


hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Nudix hydrolase domain-containing protein / Nudix hydrolase domain-containing protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
CitationJournal: Biochemistry / Year: 2014
Title: Chlamydia trachomatis CT771 (nudH) Is an Asymmetric Ap4A Hydrolase.
Authors: Barta, M.L. / Lovell, S. / Sinclair, A.N. / Battaile, K.P. / Hefty, P.S.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references / Other
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

Downloads & links

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Assembly

Deposited unit
A: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8563
Polymers17,6681
Non-polymers1882
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.351, 116.351, 84.112
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 CT771


Mass: 17667.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / ATCC VR-902B / Gene: CTL0140 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B0B8Z7, UniProt: A0A0H3MCJ9*PLUS, Hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.65 Å3/Da / Density % sol: 73.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.0, 1.5 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→64.57 Å / Num. all: 10818 / Num. obs: 10818 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 19.1 % / Biso Wilson estimate: 71.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 30.9
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 20.4 % / Rmerge(I) obs: 1.516 / Mean I/σ(I) obs: 2.2 / Rsym value: 1.516 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I7V

3i7v


Resolution: 2.6→38.085 Å / Occupancy max: 1 / Occupancy min: 0.94 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 520 4.82 %
Rwork0.1906 --
obs0.1919 10788 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.6741 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 11 9 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131206
X-RAY DIFFRACTIONf_angle_d1.1391637
X-RAY DIFFRACTIONf_dihedral_angle_d16.244416
X-RAY DIFFRACTIONf_chiral_restr0.076173
X-RAY DIFFRACTIONf_plane_restr0.006215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.86160.29161300.23192485X-RAY DIFFRACTION100
2.8616-3.27550.31991130.22982534X-RAY DIFFRACTION100
3.2755-4.1260.18831300.19182553X-RAY DIFFRACTION100
4.126-38.08890.2041470.17542696X-RAY DIFFRACTION100
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)
12.67932.50860.36086.551-0.48893.0524-0.24480.61090.1669-0.43130.68450.52011.694-0.4914-0.39060.8924-0.0531-0.21740.2661-0.10140.5286-53.616813.87115.7476
22.0439-3.6146.89163.1771-0.57875.94990.40883.96690.7456-0.68210.6196-0.6210.31591.3266-0.50091.299-0.072-0.16941.14460.05680.6016-51.29027.6485-6.703
39.45220.7372-1.45266.5528-2.76237.85890.62930.93210.3719-1.2464-0.08511.1317-0.06120.0787-0.61070.711-0.0515-0.14340.4032-0.05580.4283-51.587925.8116-3.3547
46.37740.78171.86231.4151-2.77638.28270.12260.25470.3616-0.33320.35910.5460.467-0.4693-0.42910.52710.0045-0.11080.23510.01680.5536-56.849222.85064.588
51.3115-0.969-3.53920.55191.93572.20490.32370.479-0.8987-2.2296-0.64130.38431.60770.73580.01951.45960.4801-0.0470.8693-0.29090.6174-39.495417.9195-4.8399
64.38792.59160.34845.8309-2.11398.19680.33090.1333-0.3623-0.51690.008-0.20340.56180.9958-0.11270.51850.0686-0.08650.302-0.14290.4511-47.089220.12821.6086
74.99830.066-2.68315.1483.05695.2759-0.41250.6483-0.2070.14090.520.28811.57180.058-0.09820.9846-0.0523-0.06890.3698-0.00260.4833-51.93788.99666.3513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 33 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 40 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 51 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 74 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 88 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 89 through 102 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 149 )A0

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