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- PDB-3nqr: A putative CBS domain-containing protein from Salmonella typhimur... -

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Basic information

Entry
Database: PDB / ID: 3nqr
TitleA putative CBS domain-containing protein from Salmonella typhimurium LT2
ComponentsMagnesium and cobalt efflux protein corC
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / CBS domain / efflux protein corC / Structure genomics
Function / homology
Function and homology information


flavin adenine dinucleotide binding / plasma membrane
Similarity search - Function
: / N-terminal region of NMB0537 / CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily ...: / N-terminal region of NMB0537 / CBS domain Like - #20 / CBS domain Like / Transporter-associated domain / Transporter associated domain / Transporter associated domain / Ion transporter-like, CBS domain / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Magnesium and cobalt efflux protein CorC
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Cui, H. / Joachimiak, A. / Anderson, F.W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: A putative CBS domain-containing protein from Salmonella typhimurium LT2.
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Cui, H. / Joachimiak, A. / Anderson, F.W.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnesium and cobalt efflux protein corC
B: Magnesium and cobalt efflux protein corC
C: Magnesium and cobalt efflux protein corC
D: Magnesium and cobalt efflux protein corC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9018
Polymers59,5134
Non-polymers1,3894
Water3,747208
1
A: Magnesium and cobalt efflux protein corC
hetero molecules

D: Magnesium and cobalt efflux protein corC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4514
Polymers29,7562
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area3050 Å2
ΔGint-17 kcal/mol
Surface area13300 Å2
MethodPISA
2
B: Magnesium and cobalt efflux protein corC
hetero molecules

C: Magnesium and cobalt efflux protein corC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4514
Polymers29,7562
Non-polymers6942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area3790 Å2
ΔGint-20 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.123, 54.122, 92.119
Angle α, β, γ (deg.)90.00, 94.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Magnesium and cobalt efflux protein corC


Mass: 14878.149 Da / Num. of mol.: 4 / Fragment: CBS domain residues 65-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: corC, STM0667 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: P0A2L3
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 25% w/v PEG4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2010 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 34373 / Num. obs: 34373 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.72
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.08 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARPWARPmodel building
Cootmodel building
CCP4model building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.874 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25833 1735 5 %RANDOM
Rwork0.19009 ---
obs0.19351 32639 98.91 %-
all-32639 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.581 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20.06 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 92 208 4245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224101
X-RAY DIFFRACTIONr_bond_other_d0.0010.022862
X-RAY DIFFRACTIONr_angle_refined_deg1.9672.0115528
X-RAY DIFFRACTIONr_angle_other_deg1.00136967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1175490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.85623.297182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61815799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5721543
X-RAY DIFFRACTIONr_chiral_restr0.1190.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
X-RAY DIFFRACTIONr_mcbond_it1.671.52468
X-RAY DIFFRACTIONr_mcbond_other0.5151.5988
X-RAY DIFFRACTIONr_mcangle_it3.0224027
X-RAY DIFFRACTIONr_scbond_it4.94631633
X-RAY DIFFRACTIONr_scangle_it7.6484.51501
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 117 -
Rwork0.209 2248 -
obs--93.96 %
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)
10.7651-0.5976-0.51461.6042-0.24810.7186-0.04950.04-0.04890.06190.0240.06540.019-0.05450.02550.09030.004-0.00290.0606-0.00590.03842.0026-2.432531.0365
21.38440.59590.0710.27130.14720.95880.05340.092-0.1610.02640.0312-0.0829-0.02080.0036-0.08460.04360.0105-0.03590.05980.00790.086338.5162-7.4091-3.7347
30.5715-0.5515-0.08170.53580.11461.6460.0316-0.0310.0378-0.01950.0509-0.0366-0.0323-0.0656-0.08250.0327-0.0114-0.00060.07290.00960.085335.248413.07724.9838
40.7471-0.1796-0.66681.3250.22560.70370.00730.0360.0362-0.0131-0.06640.0120.0639-0.02760.05910.1014-0.00150.01160.04590.00720.084450.83610.722453.9546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A67 - 192
2X-RAY DIFFRACTION2B65 - 190
3X-RAY DIFFRACTION3C66 - 191
4X-RAY DIFFRACTION4D67 - 189

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