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- PDB-6c1e: NavAb NormoPP mutant -

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Basic information

Entry
Database: PDB / ID: 6c1e
TitleNavAb NormoPP mutant
ComponentsIon transport proteinIon transporter
KeywordsMETAL TRANSPORT / Mutant
Function / homology
Function and homology information


monoatomic cation channel activity / identical protein binding / plasma membrane
Similarity search - Function
Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Chem-BNC / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-UHH / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsCatterall, W.A. / Zheng, N. / Jiang, D. / Gamal El-Din, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)NS015751 United States
CitationJournal: Nature / Year: 2018
Title: Structural basis for gating pore current in periodic paralysis.
Authors: Jiang, D. / Gamal El-Din, T.M. / Ing, C. / Lu, P. / Pomes, R. / Zheng, N. / Catterall, W.A.
History
DepositionJan 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,00122
Polymers66,0102
Non-polymers12,99120
Water0
1
A: Ion transport protein
B: Ion transport protein
hetero molecules

A: Ion transport protein
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,00244
Polymers132,0204
Non-polymers25,98240
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area42610 Å2
ΔGint-259 kcal/mol
Surface area41100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.775, 126.997, 192.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ion transport protein / Ion transporter


Mass: 33004.949 Da / Num. of mol.: 2 / Mutation: C235I, H123R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria)
Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical ChemComp-BNC / 5-BETA-24-NOR-CHOLANE-3(ALPHA),7(ALPHA),12(ALPHA)-TRIOL


Mass: 364.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H40O3
#4: Chemical ChemComp-UHH / (3ALPHA,5ALPHA,7ALPHA,8ALPHA,12ALPHA,14BETA,17ALPHA)-3,7,12-TRIHYDROXYCHOL-1-EN-24-AMIDE


Mass: 405.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H39NO4

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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: 5.86 Å3/Da / Density % sol: 79.02 %
Crystal growTemperature: 277 K / Method: evaporation / Details: ammonium sulphate, Na-citrate / PH range: 4.8-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99994 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.86→42.5 Å / Num. obs: 35059 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 16.6
Reflection shellResolution: 2.86→3 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY

3rvy


Resolution: 2.86→42.5 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.29
RfactorNum. reflection% reflection
Rfree0.2399 1763 5.03 %
Rwork0.2125 --
obs0.2139 35059 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.86→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 512 0 4118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014208
X-RAY DIFFRACTIONf_angle_d1.315646
X-RAY DIFFRACTIONf_dihedral_angle_d20.6391584
X-RAY DIFFRACTIONf_chiral_restr0.052636
X-RAY DIFFRACTIONf_plane_restr0.005618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8575-2.93480.3254730.29671478X-RAY DIFFRACTION57
2.9348-3.02110.37341400.2842602X-RAY DIFFRACTION100
3.0211-3.11860.3131390.28832648X-RAY DIFFRACTION100
3.1186-3.230.30681280.27352623X-RAY DIFFRACTION100
3.23-3.35930.28551570.24692600X-RAY DIFFRACTION100
3.3593-3.51210.25741310.23432626X-RAY DIFFRACTION100
3.5121-3.69720.23831230.19912643X-RAY DIFFRACTION100
3.6972-3.92870.24531530.19352613X-RAY DIFFRACTION100
3.9287-4.23180.2121560.17172651X-RAY DIFFRACTION100
4.2318-4.65710.16791410.1712640X-RAY DIFFRACTION100
4.6571-5.32990.19741430.17572680X-RAY DIFFRACTION100
5.3299-6.71090.27361330.25732700X-RAY DIFFRACTION100
6.7109-42.50420.25561460.21892792X-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)
14.02230.3848-0.83443.93772.16215.64290.1920.00150.5784-0.2307-0.58810.9578-1.7261-0.8550.45050.77380.15930.16681.0736-0.16151.229434.6776154.842127.704
22.78690.18090.15751.3293-0.40852.9926-0.1622-0.5273-0.39110.6645-0.58731.16820.173-0.10570.32621.41050.48470.46051.0711-0.56811.59140.4768162.290529.3457
33.0118-0.63330.91244.43170.06224.01060.01560.59650.46930.2298-0.47091.1173-0.13320.44310.07350.90580.04840.17751.4742-0.26691.353448.9474160.011723.4768
45.5625-0.55661.22522.5670.2952.36-0.0564-0.91930.285-0.29740.01940.1827-0.4165-0.38040.03540.97580.1630.16290.8196-0.2170.9548.9555148.978930.305
52.85690.04431.34413.44420.942.1835-0.1618-0.18750.4414-0.06290.2145-0.1562-0.14710.0414-0.04650.4065-0.0379-0.03340.4195-0.07020.507375.2225136.204418.9972
65.3572-3.3739-4.56483.93160.84546.39070.42570.03880.2114-0.7490.32111.157-0.33410.6108-0.19411.7021-0.15240.37081.34450.17551.282724.323798.538643.4101
73.7339-0.2226-0.45672.9303-0.75712.3432-0.57840.7569-0.9691-1.51780.47330.32131.6723-1.6136-0.28691.2585-0.22020.18780.58530.09221.15139.811398.167221.6642
81.7939-1.7677-1.14492.56422.88037.4788-0.82270.266-0.9860.0987-0.3414-0.4520.24-0.03330.44541.1627-0.58750.63161.38170.34491.726729.0511100.4324.9237
94.34490.686-0.16973.5122-0.59081.8982-0.0742-1.3695-0.85040.1023-0.120.275-0.8546-0.4664-0.30521.1946-0.14030.26881.03570.29921.079128.9893112.682328.8257
101.37610.3284-0.19993.76460.64672.20310.1499-0.3219-0.17180.6068-0.2730.09980.2095-0.40280.08250.3949-0.03290.08120.78050.06580.703644.3212125.406327.1894
112.53881.5156-3.66454.71281.2289.79660.2191.93540.1144-1.40040.08620.9671-0.0392-0.1585-0.55870.64910.2153-0.12850.81620.0520.701349.9051140.85845.2032
122.6449-0.102-0.38843.55021.12882.21780.0418-0.23880.22230.7910.03440.39710.0319-0.0191-0.00080.5794-0.00440.06110.4359-0.01830.506657.5328137.613319.665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1001 through 1041 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1042 through 1074 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1075 through 1096 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1097 through 1127 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1128 through 1221 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2001 through 2011 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2012 through 2041 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2042 through 2065 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2066 through 2096 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2097 through 2152 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2153 through 2162 )
12X-RAY DIFFRACTION12chain 'B' and (resid 2163 through 2221 )

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