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- PDB-2ipq: Crystal structure of C-terminal domain of Salmonella Enterica pro... -

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Basic information

Entry
Database: PDB / ID: 2ipq
TitleCrystal structure of C-terminal domain of Salmonella Enterica protein STY4665, PFAM DUF1528
ComponentsHypothetical protein STY4665
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


STY4665 C-terminal domain-like / Integrating conjugative element relaxase, PFGI-1 class / Uncharacterised domain, helicase/relaxase, putative / Putative helicase / Putative conjugal transfer nickase/helicase TraI, C-terminal / Putative conjugal transfer nickase/helicase TraI C-term / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Thrombin, subunit H / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...STY4665 C-terminal domain-like / Integrating conjugative element relaxase, PFGI-1 class / Uncharacterised domain, helicase/relaxase, putative / Putative helicase / Putative conjugal transfer nickase/helicase TraI, C-terminal / Putative conjugal transfer nickase/helicase TraI C-term / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Thrombin, subunit H / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsRamagopal, U.A. / Bonanno, J.B. / Gilmore, J. / Toro, R. / Bain, K.T. / Reyes, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of C-terminal domain of Hypothetical protein STY4665
Authors: Ramagopal, U.A. / Bonanno, J.B. / Gilmore, J. / Toro, R. / Bain, K.T. / Reyes, C. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
History
DepositionOct 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Hypothetical protein STY4665


Theoretical massNumber of molelcules
Total (without water)15,4831
Polymers15,4831
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.281, 55.039, 66.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein STY4665 / Hypothetical protein


Mass: 15483.396 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 395-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: STY4665, t4356 / Plasmid: BS-pSGX4(BS) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8Z1C5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: (NH4)2SO4 0.2 M, Bis-Tris pH 6.5 0.1 M, PEG 3350 50 %, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2006 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 3 % / Av σ(I) over netI: 10.1 / Number: 38459 / Rmerge(I) obs: 0.066 / Χ2: 1.02 / D res high: 2.2 Å / D res low: 30 Å / Num. obs: 13020 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.73309810.0371.5272.9
3.764.7399.210.0481.7363
3.293.7699.510.0571.7723
2.993.2999.810.0831.3753.1
2.772.9910010.1130.8973.1
2.612.7710010.1810.683.1
2.482.6110010.2360.5813.1
2.372.4810010.3660.5273.1
2.282.3799.910.4190.4962.9
2.22.2898.510.4910.4282.3
ReflectionResolution: 2.2→30 Å / Num. obs: 7182 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.066 / Rsym value: 0.05 / Χ2: 1.016 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1288 / Rsym value: 0.419 / Χ2: 0.428 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
SOLVEphasing
RESOLVEphasing
PHENIXphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.574 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.282 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27 336 4.7 %RANDOM
Rwork0.203 ---
all0.206 7150 --
obs0.206 7150 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---1.59 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 0 33 1011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221026
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9451382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7115124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80122.08348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.13715177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.401159
X-RAY DIFFRACTIONr_chiral_restr0.1120.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02783
X-RAY DIFFRACTIONr_nbd_refined0.2480.2394
X-RAY DIFFRACTIONr_nbtor_refined0.3280.2691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.27
X-RAY DIFFRACTIONr_mcbond_it2.1331.5625
X-RAY DIFFRACTIONr_mcangle_it2.7592982
X-RAY DIFFRACTIONr_scbond_it4.4913457
X-RAY DIFFRACTIONr_scangle_it6.1084.5400
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 25 -
Rwork0.232 462 -
obs-487 94.38 %
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)
16.961.7075-3.27127.7515-1.50494.97830.09790.47010.3753-0.2646-0.0709-0.0095-0.2494-0.1604-0.027-0.43210.0393-0.0572-0.21930.0261-0.1765-1.2418.106-15.712
27.05510.7641-3.31924.7991-0.15874.7377-0.0442-0.263-0.03250.1843-0.0402-0.2886-0.10420.08940.0844-0.37470.033-0.0363-0.1364-0.0094-0.1481-1.05511.087-10.77
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: X / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11399 - 4485 - 54
22461 - 52867 - 134

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