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- PDB-3ck6: Crystal structure of ZntB cytoplasmic domain from Vibrio parahaem... -

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Basic information

Entry
Database: PDB / ID: 3ck6
TitleCrystal structure of ZntB cytoplasmic domain from Vibrio parahaemolyticus RIMD 2210633
ComponentsPutative membrane transport protein
KeywordsSTRUCTURAL PROTEIN / APC91421.1 / ZntB / cytoplasmic domain / Vibrio parahaemolyticus RIMD 2210633 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Magnesium transport protein CorA, transmembrane region / CorA soluble domain-like / Beta Polymerase; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative membrane transport protein
Similarity search - Component
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTan, K. / Sather, A. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2009
Title: Structure and electrostatic property of cytoplasmic domain of ZntB transporter.
Authors: Tan, K. / Sather, A. / Robertson, J.L. / Moy, S. / Roux, B. / Joachimiak, A.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionMar 25, 2008ID: 3BHC
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Putative membrane transport protein
B: Putative membrane transport protein
C: Putative membrane transport protein
D: Putative membrane transport protein
E: Putative membrane transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,03230
Polymers148,1465
Non-polymers88625
Water12,070670
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-43.2 kcal/mol
Surface area51380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.390, 130.213, 79.386
Angle α, β, γ (deg.)90.00, 103.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative membrane transport protein


Mass: 29629.131 Da / Num. of mol.: 5 / Fragment: ZntB cytoplasmic domain: Residues 1-249 / Mutation: S42G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VP2389, NP_798768.1 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87M69
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris-HCl, 30% PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.28234 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 15, 2008 / Details: Mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28234 Å / Relative weight: 1
ReflectionResolution: 1.9→30.8 Å / Num. all: 97781 / Num. obs: 97781 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 23.17
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1.22 / Num. unique all: 6287 / % possible all: 81.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.883 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22347 4875 5 %RANDOM
Rwork0.1849 ---
all0.18689 92732 --
obs0.18689 92732 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.708 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0.11 Å2
2---0.57 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10008 0 25 670 10703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02110281
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.94113942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40751228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42924.268567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.569151811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4791580
X-RAY DIFFRACTIONr_chiral_restr0.0960.21516
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027962
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.24793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.27034
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2614
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.771.56331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24929958
X-RAY DIFFRACTIONr_scbond_it2.07434432
X-RAY DIFFRACTIONr_scangle_it3.2384.53977
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 284 -
Rwork0.28 5596 -
obs-5880 79.76 %
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)
11.47420.473-0.28911.4629-0.23951.02320.00040.0165-0.0377-0.0055-0.0493-0.07320.03580.0150.0489-0.23540.01260.0460.0508-0.0076-0.162314.726-61.72552.792
21.4975-0.3603-0.38430.78950.37471.22240.0366-0.06320.0901-0.0217-0.0128-0.0559-0.04880.1403-0.0237-0.2128-0.01190.02660.0510.0086-0.136915.461-30.30549.193
31.4384-0.5586-0.10171.71470.18270.6687-0.02490.070.116-0.03270.0437-0.05090.06440.0074-0.0188-0.2197-0.00920.02620.040.0129-0.134511.167-23.85918.835
41.5659-0.66050.4971.7326-0.58261.07110.06960.0996-0.0433-0.1582-0.06660.12340.04950.0834-0.003-0.1758-0.00570.02760.0305-0.0113-0.17638.468-51.083.315
51.52580.89980.27451.31880.2151.12950.0306-0.0442-0.1190.00670.0366-0.07810.04610.0957-0.0672-0.20860.01850.05830.0638-0.0047-0.155410.761-74.37324.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2444 - 247
2X-RAY DIFFRACTION2BB1 - 2444 - 247
3X-RAY DIFFRACTION3CC2 - 2435 - 246
4X-RAY DIFFRACTION4DD1 - 2444 - 247
5X-RAY DIFFRACTION5EE0 - 2443 - 247

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