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- PDB-3byp: Mode of Action of a Putative Zinc Transporter CzrB -

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Basic information

Entry
Database: PDB / ID: 3byp
TitleMode of Action of a Putative Zinc Transporter CzrB
ComponentsCzrB protein
KeywordsTRANSPORT PROTEIN / membrane protein / zinc transporter
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / membrane / identical protein binding / metal ion binding
Similarity search - Function
Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / Dimerisation domain of Zinc Transporter / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCherezov, V. / Srinivasan, V. / Szebenyi, D.M.E. / Caffrey, M.
CitationJournal: Structure / Year: 2008
Title: Insights into the Mode of Action of a Putative Zinc Transporter CzrB in Thermus thermophilus
Authors: Cherezov, V. / Hofer, N. / Szebenyi, D.M. / Kolaj, O. / Wall, J.G. / Gillilan, R. / Srinivasan, V. / Jaroniec, C.P. / Caffrey, M.
History
DepositionJan 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,8495
Polymers21,5602
Non-polymers2883
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-7 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.331, 60.331, 92.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein CzrB protein


Mass: 10780.223 Da / Num. of mol.: 2 / Fragment: sequence database residues 198-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: czrB / Plasmid: pIVEX2.4d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8VLX7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.25 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / pH: 4.6
Details: Protein solution 15 mg/ml protein, 20mM Tris, pH 8.0; precipitant solution 0.2M ammonium sulfate, 15% PEG 4000, 0.1M sodium acetate, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2006
RadiationMonochromator: BENT SINGLE-CRYSTAL SI(111), WITH FOCUSING MIRROR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9124 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 21179 / % possible obs: 98.9 % / Redundancy: 12.8 % / Rsym value: 0.042 / Net I/σ(I): 54.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.393 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CZRB WITH ZN BOUND

Resolution: 1.7→30.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.791 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 2 TLS GROUPS USED
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1086 5.1 %RANDOM
Rwork0.186 ---
all-20053 --
obs-20053 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å20 Å2
2---0.41 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 15 296 1621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211375
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9851855
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6615162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.79421.79578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40415241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0971524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021072
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2631
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2918
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.5848
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29921320
X-RAY DIFFRACTIONr_scbond_it2.5743565
X-RAY DIFFRACTIONr_scangle_it4.1274.5535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 78 -
Rwork0.225 1355 -
obs--92.1 %
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)
15.6135-2.12242.32531.471-0.71091.0055-0.0368-0.2311-0.22160.11620.08630.0319-0.0297-0.1617-0.0495-0.05990.02390.02080.01080.0444-0.06317.25849.4910.445
21.963-0.2989-0.74710.30270.65242.83390.0175-0.04810.00460.1-0.0370.01970.19610.04380.0195-0.0022-0.01390.021-0.0704-0.0106-0.0376-17.16558.11314.239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 876 - 87
2X-RAY DIFFRACTION2BB6 - 876 - 87

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