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- PDB-3kzg: Crystal structure of an arginine 3rd transport system periplasmic... -

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Basic information

Entry
Database: PDB / ID: 3kzg
TitleCrystal structure of an arginine 3rd transport system periplasmic binding protein from Legionella pneumophila
ComponentsArginine 3rd transport system periplasmic binding protein
KeywordsTRANSPORT PROTEIN / Arginine transport system / Periplasmic binding protein / Legionella pneumophila / Protein Structure Initiative II(PSI II) / NYSGXRC / 11316i / Structural Genomics / New York SGX Research Center for Structural Genomics
Function / homologyBacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Arginine 3rd transport system periplasmic binding protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å
AuthorsPalani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an arginine 3rd transport system periplasmic binding protein from Legionella pneumophila
Authors: Palani, K. / Burley, S.K. / Swaminathan, S.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 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
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Arginine 3rd transport system periplasmic binding protein
B: Arginine 3rd transport system periplasmic binding protein
C: Arginine 3rd transport system periplasmic binding protein
D: Arginine 3rd transport system periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)111,5664
Polymers111,5664
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Arginine 3rd transport system periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)27,8921
Polymers27,8921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Arginine 3rd transport system periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)27,8921
Polymers27,8921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Arginine 3rd transport system periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)27,8921
Polymers27,8921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Arginine 3rd transport system periplasmic binding protein


Theoretical massNumber of molelcules
Total (without water)27,8921
Polymers27,8921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.965, 148.254, 149.262
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
Arginine 3rd transport system periplasmic binding protein


Mass: 27891.518 Da / Num. of mol.: 4 / Fragment: sequence database residues 18-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: strain Philadelphia 1/ATCC 33152/DSM 7513 / Gene: artJ, lpg1555 / Plasmid: BC-pSGX3(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZV85
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.1M Bis-Tris, 0.2M Lithium sulfate monohydrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2009 / Details: MIRRORS
RadiationMonochromator: SI(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→41.31 Å / Num. all: 58467 / Num. obs: 58467 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.2
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5708 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.06→41.31 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 64845.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2925 5.1 %RANDOM
Rwork0.221 ---
obs0.221 57836 98.7 %-
all-58467 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7422 Å2 / ksol: 0.381474 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2---5.17 Å20 Å2
3---2.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.06→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 0 382 7786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.78
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.06→2.19 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 459 5 %
Rwork0.221 8642 -
obs-5708 94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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