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- PDB-2i4b: Crystal structure of Bicarbonate Transport Protein CmpA from Syne... -

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Basic information

Entry
Database: PDB / ID: 2i4b
TitleCrystal structure of Bicarbonate Transport Protein CmpA from Synechocystis sp. PCC 6803 in complex with bicarbonate and calcium
ComponentsBicarbonate transporterAnion exchanger family
KeywordsTRANSPORT PROTEIN / alpha-beta protein / C-clamp / periplasmic solute-binding protein / ABC transporter / bicarbonate
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
BICARBONATE ION / Bicarbonate-binding protein CmpA
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.35 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 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)47,1873
Polymers47,0861
Non-polymers1012
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.790, 49.570, 57.740
Angle α, β, γ (deg.)87.670, 81.230, 75.240
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Bicarbonate transporter / Anion exchanger family


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-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Fragment: Ca2+ ion / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Fragment: bicarbonate / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 298 K / Method: batch/microseeding / pH: 8
Details: Ammonium sulfate, HEPPS, EGTA, NaHCO3, pH 8.0, batch/microseeding, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 1, 2006 / Details: Helios
RadiationMonochromator: Helios multilayer, double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.35→24.6 Å / Num. all: 102903 / Num. obs: 102903 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rsym value: 0.042 / Net I/σ(I): 24.9
Reflection shellResolution: 1.35→1.44 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.196 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2I48

2i48


Resolution: 1.35→24.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 10343 9.9 %random
Rwork0.209 ---
all0.209 102903 --
obs0.209 102903 98.7 %-
Solvent computationBsol: 46.191 Å2
Displacement parametersBiso mean: 12.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.708 Å2-0.12 Å20.466 Å2
2--1.441 Å2-0.712 Å2
3----0.733 Å2
Refinement stepCycle: LAST / Resolution: 1.35→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 5 421 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it0.861.5
X-RAY DIFFRACTIONc_scbond_it1.8482
X-RAY DIFFRACTIONc_mcangle_it1.2052
X-RAY DIFFRACTIONc_scangle_it2.0362.5
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 DIFFRACTION5hco3.paramhco3.top

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