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- PDB-2i48: Crystal structure of Bicarbonate Transport Protein CmpA from Syne... -

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Basic information

Entry
Database: PDB / ID: 2i48
TitleCrystal structure of Bicarbonate Transport Protein CmpA from Synechocystis sp. PCC 6803 in complex with carbonic acid
ComponentsBicarbonate transporter
KeywordsTRANSPORT PROTEIN / alpha-beta protein / C-clamp / ABC transporter / periplasmic solute-binding protein / bicarbonate-binding protein
Function / homology
Function and homology information


monoatomic ion transport / plasma membrane
Similarity search - Function
Nitrate/bicarbonate ABC transporter substrate-binding domain / NMT1-like family / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Bicarbonate-binding protein CmpA
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKoropatkin, N.M. / Smith, T.J. / Pakrasi, H.B.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA.
Authors: Koropatkin, N.M. / Koppenaal, D.W. / Pakrasi, H.B. / Smith, T.J.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Bicarbonate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1462
Polymers47,0861
Non-polymers601
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.540, 49.640, 57.780
Angle α, β, γ (deg.)87.330, 80.500, 75.310
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bicarbonate transporter


Mass: 47085.863 Da / Num. of mol.: 1 / Fragment: solute-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: cmpA / Plasmid: pET-28rTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q55460
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Fragment: carbonic acid / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: batch/microseeding / pH: 5
Details: Ammonium sulfate, succinate, sodium carbonate, pH 5.0, batch/microseeding, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899, 0.97915, 0.97132
DetectorType: SBC-3 / Detector: CCD / Date: Nov 3, 2005 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979151
30.971321
ReflectionResolution: 1.6→40 Å / Num. all: 56952 / Num. obs: 56952 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rsym value: 0.077 / Net I/σ(I): 22.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 14.1 / Rsym value: 0.7 / % possible all: 89.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→37.02 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 5797 9.3 %random
Rwork0.175 ---
all0.175 56952 --
obs0.175 56952 91.4 %-
Solvent computationBsol: 47.536 Å2
Displacement parametersBiso mean: 13.158 Å2
Baniso -1Baniso -2Baniso -3
1--4.006 Å20.955 Å22.129 Å2
2--3.541 Å2-0.645 Å2
3---0.465 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 4 393 3520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.309
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_scbond_it1.6342
X-RAY DIFFRACTIONc_mcangle_it1.2282
X-RAY DIFFRACTIONc_scangle_it2.1872.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CO3.paramCO3.top

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