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- PDB-3lfr: The Crystal Structure of a CBS Domain from a Putative Metal Ion T... -

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Basic information

Entry
Database: PDB / ID: 3lfr
TitleThe Crystal Structure of a CBS Domain from a Putative Metal Ion Transporter Bound to AMP from Pseudomonas syringae to 1.55A
Componentsputative Metal ion transporterZinc transporter protein
KeywordsTRANSPORT PROTEIN / Metal-ion / CBS / AMP / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative
Function / homology
Function and homology information


flavin adenine dinucleotide binding
Similarity search - Function
CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain ...CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Metal ion transporter, putative
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 Å
AuthorsStein, A.J. / Bigelow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of a CBS Domain from a Putative Metal Ion Transporter Bound to AMP from Pseudomonas syringae to 1.55A
Authors: Stein, A.J. / Bigelow, L. / Cobb, G. / Joachimiak, A.
History
DepositionJan 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative Metal ion transporter
B: putative Metal ion transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1864
Polymers30,4922
Non-polymers6942
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-21 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.150, 50.650, 51.867
Angle α, β, γ (deg.)90.000, 112.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative Metal ion transporter / Zinc transporter protein


Mass: 15245.927 Da / Num. of mol.: 2 / Fragment: residues 59-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Strain: pv. tomato str. DC3000 / Gene: PSPTO4807, PSPTO_4807 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87VX8
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.1M Hepes PH 7.5, 0.2M Lithium sulfate, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 33409 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.102 / Χ2: 7.265 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.55-1.613.10.65232993.45199.7
1.61-1.673.10.45933512.67399.7
1.67-1.753.10.34333383.33999.8
1.75-1.843.10.24333623.25899.9
1.84-1.953.10.1833253.8799.9
1.95-2.13.10.13133564.75699.6
2.1-2.323.10.11533577.27499.8
2.32-2.653.10.109337310.06799.6
2.65-3.3430.087336413.99599.5
3.34-503.10.073328420.48994.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.53→34.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.182 / SU B: 3.434 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1678 5.1 %RANDOM
Rwork0.175 ---
obs0.177 33130 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.13 Å2
2--0.08 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.53→34.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 46 172 2171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222038
X-RAY DIFFRACTIONr_angle_refined_deg1.4812.0192790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42123.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31115347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9011516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211484
X-RAY DIFFRACTIONr_mcbond_it1.1291.51276
X-RAY DIFFRACTIONr_mcangle_it1.89122077
X-RAY DIFFRACTIONr_scbond_it3.0123762
X-RAY DIFFRACTIONr_scangle_it4.5394.5707
X-RAY DIFFRACTIONr_rigid_bond_restr1.41732038
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.534-1.5740.2811110.2031994250484.065
1.574-1.6170.2651060.1792216239596.952
1.617-1.6640.2371030.1662207234998.34
1.664-1.7150.2331090.1612149229898.259
1.715-1.7710.2181080.1642106224498.663
1.771-1.8330.1861100.1482042216999.216
1.833-1.9020.227920.1571979208499.376
1.902-1.9790.2321120.1661897201499.752
1.979-2.0670.205930.1711825192799.533
2.067-2.1670.206900.1681720182299.341
2.167-2.2840.226970.1611657175699.886
2.284-2.4220.226810.1761591167899.642
2.422-2.5880.254840.1931470156199.552
2.588-2.7950.228750.1931374145799.451
2.795-3.0590.259770.1871253134099.254
3.059-3.4170.189580.1741165122499.918
3.417-3.9390.155600.1571017108799.08
3.939-4.8090.185440.16284692196.634
4.809-6.7380.177400.2165772496.271
6.738-34.8410.248280.22328742773.77

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