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- PDB-3q17: Structure of a slow CLC Cl-/H+ antiporter from a cyanobacterium i... -

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Basic information

Entry
Database: PDB / ID: 3q17
TitleStructure of a slow CLC Cl-/H+ antiporter from a cyanobacterium in Bromide
ComponentsSll0855 protein
KeywordsTRANSPORT PROTEIN / CLC Cl-/H+ exchange transporter / CLC family / cyanobacterium / transporter / integral membrane protein / CLC_Ec1 / chloride proton antiport
Function / homology
Function and homology information


voltage-gated chloride channel activity / membrane
Similarity search - Function
Clc chloride channel / Clc chloride channel / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Sll0855 protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsJayaram, H. / Robertson, J.L. / Fang, W. / Williams, C. / Miller, C.
CitationJournal: Biochemistry / Year: 2011
Title: Structure of a Slow CLC Cl(-)/H(+) Antiporter from a Cyanobacterium.
Authors: Jayaram, H. / Robertson, J.L. / Wu, F. / Williams, C. / Miller, C.
History
DepositionDec 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Sll0855 protein
B: Sll0855 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3704
Polymers100,2102
Non-polymers1602
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-64 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.209, 207.209, 105.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Sll0855 protein / CLC Cl-/H+ exchange transporter / CLC_SY1


Mass: 50105.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: sll0855, syn:sll0855 / Plasmid: pAsk / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73745
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br

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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: 6.554019 Å3/Da / Density % sol: 81.232887 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 30% PEG400, 0.1 M Tris-HBr, 0.2 M CaCl2 with 14 mM C-Hega-11, 6.2% PEG400 added to protein, pH 8.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9199
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9199 Å / Relative weight: 1
ReflectionResolution: 3.6→68.479 Å / Num. all: 30660 / Num. obs: 29893 / % possible obs: 97.8 % / Redundancy: 16.8 % / Rsym value: 0.257 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.6-3.7916.40.0160.51.57196.9
3.79-4.0216.30.0160.71.103196.9
4.02-4.316.30.0161.30.591196.8
4.3-4.6516.20.01620.389196.6
4.65-5.0916.10.0162.30.328196.7
5.09-5.6916.10.0162.40.315198.8
5.69-6.5716.90.0162.50.31100
6.57-8.05180.0164.60.1511100
8.05-11.3820.60.0167.10.091100
11.38-74.08519.60.01630.099199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.02 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.6 Å68.48 Å
Translation3.6 Å68.48 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
MOSFLMdata reduction
SCALA3.3.16data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ND0

3nd0


Resolution: 3.6→68.479 Å / Cor.coef. Fo:Fc: 0.79 / Cor.coef. Fo:Fc free: 0.758 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 0.1 / Phase error: 33.8 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.3102 1492 5 %
Rwork0.2805 --
obs0.2819 29827 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.317 Å2 / ksol: 0.268 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--29.0273 Å20 Å20 Å2
2---29.0273 Å2-0 Å2
3---58.0547 Å2
Refinement stepCycle: LAST / Resolution: 3.6→68.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 2 0 6400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036552
X-RAY DIFFRACTIONf_angle_d0.7088914
X-RAY DIFFRACTIONf_dihedral_angle_d13.2582308
X-RAY DIFFRACTIONf_chiral_restr0.0421060
X-RAY DIFFRACTIONf_plane_restr0.0051102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.71620.45331420.38882500X-RAY DIFFRACTION96
3.7162-3.8490.33251220.34432550X-RAY DIFFRACTION96
3.849-4.00310.35641370.33322513X-RAY DIFFRACTION96
4.0031-4.18530.29271340.28892503X-RAY DIFFRACTION96
4.1853-4.40590.27281330.25322543X-RAY DIFFRACTION96
4.4059-4.68190.27521130.2432538X-RAY DIFFRACTION97
4.6819-5.04330.25241310.23052530X-RAY DIFFRACTION96
5.0433-5.55060.26421530.23892581X-RAY DIFFRACTION98
5.5506-6.35330.32511350.25132644X-RAY DIFFRACTION100
6.3533-8.00250.25391400.21222697X-RAY DIFFRACTION100
8.0025-68.49130.30921520.29742736X-RAY DIFFRACTION99
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)
11.1745-0.39260.03710.98640.1240.0249-0.1019-0.01480.3877-0.1570.0885-0.74990.0830.0147-0.00010.7321-0.10230.03120.7445-0.02541.0575-65.864764.7182.0613
20.36380.1039-0.23790.58660.26040.3392-0.0354-0.27780.10410.30760.1193-0.934-0.02430.1317-00.9636-0.0221-0.31160.9996-0.13651.1773-74.361884.276532.6109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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