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- PDB-8j1m: Crystal structure of a crosslinked variant of BbZIP -

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Basic information

Entry
Database: PDB / ID: 8j1m
TitleCrystal structure of a crosslinked variant of BbZIP
ComponentsPutative membrane protein
KeywordsMEMBRANE PROTEIN / Transporter / Zinc / Cadmium / Mercury / Crosslink
Function / homologyZinc/iron permease / ZIP Zinc transporter / zinc ion transmembrane transporter activity / plasma membrane / : / : / Chem-MPG / Zinc transporter ZIPB
Function and homology information
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å
AuthorsZhang, T. / Zhang, Y. / Sui, D. / Hu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM140931 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115373 United States
CitationJournal: Biorxiv / Year: 2024
Title: Molecular insights into substrate translocation in an elevator-type metal transporter.
Authors: Zhang, Y. / Jafari, M. / Zhang, T. / Sui, D. / Sagresti, L. / Merz Jr., K.M. / Hu, J.
History
DepositionApr 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,32912
Polymers28,9371
Non-polymers2,39111
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-73 kcal/mol
Surface area13060 Å2
Unit cell
Length a, b, c (Å)116.407, 51.012, 51.817
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative membrane protein


Mass: 28937.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Gene: BB2405 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H3LM39

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase
Details: 100 mM NaCl, 100 mM CaCl2, pH 7.0 100 mM HEPES, 30% PEG 400

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 36630 / % possible obs: 96.39 % / Redundancy: 5.5 % / Rrim(I) all: 0.179 / Net I/σ(I): 14.35
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 1471 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.952→30.441 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 3717 10.15 %
Rwork0.1712 --
obs0.1742 36630 92.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→30.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 131 58 2192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012208
X-RAY DIFFRACTIONf_angle_d0.9722964
X-RAY DIFFRACTIONf_dihedral_angle_d14.2611292
X-RAY DIFFRACTIONf_chiral_restr0.049367
X-RAY DIFFRACTIONf_plane_restr0.007370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.952-1.97630.3371720.329472X-RAY DIFFRACTION37
1.9763-2.00230.3292790.2878783X-RAY DIFFRACTION58
2.0023-2.02970.32331130.2746871X-RAY DIFFRACTION67
2.0297-2.05870.28811190.26731027X-RAY DIFFRACTION80
2.0587-2.08940.28441070.26561147X-RAY DIFFRACTION85
2.0894-2.12210.2841390.2531226X-RAY DIFFRACTION90
2.1221-2.15680.31811310.26971216X-RAY DIFFRACTION94
2.1568-2.1940.25671520.2221276X-RAY DIFFRACTION96
2.194-2.23390.271410.2041290X-RAY DIFFRACTION98
2.2339-2.27690.21981520.19371333X-RAY DIFFRACTION99
2.2769-2.32330.19541350.17991292X-RAY DIFFRACTION100
2.3233-2.37380.21041430.18151320X-RAY DIFFRACTION100
2.3738-2.4290.19711700.17191322X-RAY DIFFRACTION100
2.429-2.48970.1891350.17571276X-RAY DIFFRACTION100
2.4897-2.5570.20551470.17471342X-RAY DIFFRACTION100
2.557-2.63220.19131580.16151309X-RAY DIFFRACTION100
2.6322-2.71710.20611520.14591330X-RAY DIFFRACTION100
2.7171-2.81420.20871490.15721320X-RAY DIFFRACTION100
2.8142-2.92680.17021450.14551318X-RAY DIFFRACTION100
2.9268-3.05990.16331500.15411303X-RAY DIFFRACTION100
3.0599-3.2210.17011380.15321336X-RAY DIFFRACTION100
3.221-3.42260.18721500.15621346X-RAY DIFFRACTION100
3.4226-3.68640.2141530.1581314X-RAY DIFFRACTION100
3.6864-4.05660.21771400.16451306X-RAY DIFFRACTION100
4.0566-4.64180.19411430.17151206X-RAY DIFFRACTION91
4.6418-5.84150.19621640.1781306X-RAY DIFFRACTION100
5.8415-30.4410.14681400.1431326X-RAY DIFFRACTION100

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