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- PDB-4gqz: Crystal Structure of S.CueP -

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Basic information

Entry
Database: PDB / ID: 4gqz
TitleCrystal Structure of S.CueP
ComponentsPutative periplasmic or exported protein
KeywordsMETAL BINDING PROTEIN / CueP / V-shape dimer / Copper_resistance
Function / homologyImmunoglobulin-like - #3700 / : / Periplasmic copper-binding protein CueP / Immunoglobulin-like / Sandwich / Mainly Beta / Periplasmic or exported protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.799 Å
AuthorsHa, N.C. / Yoon, B.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium
Authors: Yoon, B.-Y. / Kim, Y.-H. / Kim, N. / Yun, B.-Y. / Kim, J.-S. / Lee, J.-H. / Cho, H.-S. / Lee, K. / Ha, N.-C.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 13, 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: Putative periplasmic or exported protein
B: Putative periplasmic or exported protein
C: Putative periplasmic or exported protein
D: Putative periplasmic or exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7856
Polymers71,7144
Non-polymers712
Water8,719484
1
A: Putative periplasmic or exported protein
B: Putative periplasmic or exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8923
Polymers35,8572
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-17 kcal/mol
Surface area14610 Å2
MethodPISA
2
C: Putative periplasmic or exported protein
D: Putative periplasmic or exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8923
Polymers35,8572
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-17 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.456, 102.160, 114.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative periplasmic or exported protein / CueP


Mass: 17928.455 Da / Num. of mol.: 4 / Fragment: UNP residues 21-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM3650 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZL99
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2.0M sodium chloride , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9790, 0.9792, 0.9900
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 30, 2011
RadiationMonochromator: double mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.991
ReflectionResolution: 1.799→50 Å / Num. obs: 118693 / % possible obs: 19.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.89 Å2
Reflection shellResolution: 1.8→1.83 Å / % possible all: 81.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.799→40.854 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.746 / SU ML: 0.23 / σ(F): 1.45 / Phase error: 31.71 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 3679 3.1 %random
Rwork0.2279 ---
obs0.2294 118692 96.75 %-
all-122680 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.66 Å2 / Biso mean: 25.8548 Å2 / Biso min: 12.86 Å2
Refinement stepCycle: LAST / Resolution: 1.799→40.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4915 0 2 484 5401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085046
X-RAY DIFFRACTIONf_angle_d1.126852
X-RAY DIFFRACTIONf_chiral_restr0.081766
X-RAY DIFFRACTIONf_plane_restr0.005888
X-RAY DIFFRACTIONf_dihedral_angle_d16.2821848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7993-1.8230.34191000.33863257335771
1.823-1.84790.31241230.33713803392684
1.8479-1.87430.35421310.32274041417288
1.8743-1.90230.36921380.31384251438993
1.9023-1.9320.38011400.28964382452296
1.932-1.96370.29731490.28094488463798
1.9637-1.99760.30671420.27164476461898
1.9976-2.03390.32491360.25594507464399
2.0339-2.0730.31531480.24624561470999
2.073-2.11530.27511460.23014468461499
2.1153-2.16130.25311440.23214572471699
2.1613-2.21160.29971470.22524540468799
2.2116-2.26690.2781490.21694527467699
2.2669-2.32820.28671440.22314536468099
2.3282-2.39670.29551460.228145184664100
2.3967-2.4740.34631440.233945764720100
2.474-2.56240.25361480.222545784726100
2.5624-2.6650.2981430.222145424685100
2.665-2.78630.25161480.226545724720100
2.7863-2.93310.30431450.229745274672100
2.9331-3.11680.27771420.224745674709100
3.1168-3.35740.31991480.212545504698100
3.3574-3.69510.27851410.201245664707100
3.6951-4.22930.23471520.191245774729100
4.2293-5.32660.20371470.189245594706100
5.3266-40.86420.23781380.25054472461098

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