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- PDB-6c1p: HypoPP mutant -

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Basic information

Entry
Database: PDB / ID: 6c1p
TitleHypoPP 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
PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Citation
Journal: 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.
#1: Journal: Nature / Year: 2011
Title: The crystal structure of a voltage-gated sodium channel.
Authors: Catterall, W.A. / Zheng, N. / Payandeh, J.
History
DepositionJan 5, 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
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,02622
Polymers132,0204
Non-polymers11,00618
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22400 Å2
ΔGint-149 kcal/mol
Surface area44180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.500, 125.552, 192.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Ion transport protein / Ion transporter


Mass: 33004.949 Da / Num. of mol.: 4 / 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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: PO4
#3: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical ChemComp-1N7 / CHAPSO / 2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium / CHAPS detergent


Mass: 631.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H59N2O8S / Comment: detergent*YM

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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: 5.73 Å3/Da / Density % sol: 78.53 %
Crystal growTemperature: 277 K / Method: evaporation / Details: ammonium sulphate, Na-citrate

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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: Sep 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.8→48.46 Å / Num. obs: 67766 / % possible obs: 98 % / Redundancy: 5.1 % / Net I/σ(I): 14.5
Reflection shellResolution: 2.8→2.9 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: 2.9→48.458 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.66 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2603 3444 5.08 %
Rwork0.2355 --
obs0.2388 67766 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7138 0 405 0 7543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127764
X-RAY DIFFRACTIONf_angle_d1.70310527
X-RAY DIFFRACTIONf_dihedral_angle_d16.7142743
X-RAY DIFFRACTIONf_chiral_restr0.0971228
X-RAY DIFFRACTIONf_plane_restr0.0081206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9004-2.95040.32671640.31943084X-RAY DIFFRACTION93
2.9504-3.0040.30481760.32823153X-RAY DIFFRACTION94
3.004-3.06170.39081780.3253215X-RAY DIFFRACTION95
3.0617-3.12420.3441390.31863171X-RAY DIFFRACTION96
3.1242-3.1920.32971710.31223204X-RAY DIFFRACTION95
3.192-3.26620.29311780.29623155X-RAY DIFFRACTION95
3.2662-3.34780.31621890.29173152X-RAY DIFFRACTION94
3.3478-3.43830.29981680.28563209X-RAY DIFFRACTION95
3.4383-3.53930.31061490.28893229X-RAY DIFFRACTION96
3.5393-3.65340.27061850.26723145X-RAY DIFFRACTION94
3.6534-3.78380.29451800.25683213X-RAY DIFFRACTION95
3.7838-3.93510.26521680.2333213X-RAY DIFFRACTION95
3.9351-4.11380.24461730.22063191X-RAY DIFFRACTION95
4.1138-4.33030.25781680.23673255X-RAY DIFFRACTION95
4.3303-4.60090.24731750.21413222X-RAY DIFFRACTION95
4.6009-4.9550.23631690.20013202X-RAY DIFFRACTION95
4.955-5.45160.24081840.21283268X-RAY DIFFRACTION95
5.4516-6.23570.2911750.24043240X-RAY DIFFRACTION95
6.2357-7.83850.28851650.24763321X-RAY DIFFRACTION95
7.8385-32.73420.20331840.19313435X-RAY DIFFRACTION95
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)
14.41351.73675.01794.4123.61176.4217-0.21220.50140.11480.47690.5844-0.9547-0.58130.7152-0.25352.6166-0.2784-0.25382.1125-0.99481.202136.7774-67.183236.8437
26.0078-0.0529-0.19522.2023-2.75083.61690.1294-0.84821.00330.08821.6004-0.1816-1.1681.5231-0.67861.0994-0.0980.16110.6066-0.56831.419722.9559-66.8263219.7565
31.822-0.7625-0.07854.7581-4.2674.19090.6229-0.28051.0663-0.16670.33930.06430.46180.2763-0.11961.4847-0.5219-0.26091.0143-0.67231.54831.4591-70.1509218.524
46.37192.83825.30525.78451.94556.0455-0.23870.77790.00520.10451.0307-1.6496-0.16681.3118-0.35961.0771-0.2351-0.20931.485-0.73671.278428.664-79.1291217.0165
51.4203-0.0002-1.0063.51580.5343.76580.4884-1.11240.16510.5181-0.5515-0.1004-0.6327-0.0938-0.01280.872-0.2649-0.11641.4236-0.03030.604215.1343-98.971221.5679
63.62480.70262.60136.60660.23382.16481.08190.9819-0.0751-0.5809-0.7994-0.94820.18220.33020.30150.84610.288-0.01060.96840.3560.489412.9282-108.1565197.7271
78.78481.1686-2.17524.0290.97781.28950.0981-0.5011-0.3539-0.11120.1672-0.2508-0.78460.0008-0.30990.6948-0.05990.00890.57480.08260.28478.16-101.7772206.9603
86.1921-0.92320.57452.7856-0.95370.57250.50820.098-2.1315-0.4678-0.16340.29680.36480.1342-0.66160.8886-0.2669-0.34570.5583-0.0250.57341.838-110.484198.1839
93.7224-1.3509-0.84271.9655-0.65952.1287-0.0065-1.4884-0.2280.48360.05850.34310.27180.4406-0.39151.4553-0.2282-0.45540.93670.2780.3213.3902-106.4371218.3595
107.61273.9785-5.91335.4591-2.45445.0569-0.41941.2115-1.1328-1.65161.3672-1.3877-0.56940.5578-0.68921.24450.0902-0.13082.6467-0.88621.278426.5184-133.3898235.6635
116.76152.3771-3.57682.44390.10373.0423-0.6025-0.65240.04830.3248-1.12410.23811.10781.70561.13531.03360.2776-0.09120.99370.21410.755926.335-118.6721219.6706
121.97810.41060.44173.7198-1.12391.6007-0.2113-0.5695-1.332-0.2848-0.0393-0.37490.4068-0.36180.09381.24690.1107-0.58671.16840.29951.213920.443-126.5273219.34
132.39381.25521.56522.12421.25358.3993-0.915-1.1786-1.48610.3258-0.8978-0.2080.41581.09371.2630.68210.1230.05921.21080.41791.334715.6772-121.9167215.4258
140.911-0.84980.89671.0071-0.56041.4059-0.671-0.7585-0.96650.78820.09720.2025-0.54490.3409-0.16571.0719-0.1508-0.15141.35250.53730.5175-7.7746-110.5684219.7712
152.3809-3.85410.24546.3731-1.21915.0320.84160.207-0.7646-1.428-0.12210.85111.9724-1.0001-1.18531.3845-0.0679-0.35230.57910.18770.2491-13.9302-107.8161196.7438
164.8909-1.59090.46575.99891.77515.33710.5762-0.5471-0.71530.0434-0.47030.4405-0.31930.4036-0.21010.555-0.215-0.00910.54870.07580.3711-8.1448-103.4496206.0532
172.7883-0.4911-0.90223.69550.10436.0383-0.2826-0.420.0042-0.22490.54820.08320.2925-0.351-0.29660.8044-0.43740.02630.88150.04250.4102-13.9042-98.5044212.8883
188.6315-3.7851-2.37055.1458-3.75477.24310.0785-1.14210.97750.55080.4386-0.8006-1.24460.9864-0.50531.79520.95920.19262.7780.03930.8757-30.0792-54.5143233.735
191.7769-0.9576-0.34247.59115.31413.75990.4103-0.2090.3443-0.226-0.13610.0897-1.7872-0.95020.17321.430.34210.4941.1892-0.24341.1863-28.1781-65.7467213.6618
203.1439-1.1613-2.0582.39942.96963.8182-0.1677-1.26160.36080.0381-0.17330.08970.0188-0.0843-0.59012.10990.64841.32381.5944-0.18551.6097-15.8722-56.279230.5403
219.5573-1.3041.53312.75512.31023.40240.27471.11290.61330.457-0.86150.6838-0.7533-0.72940.60860.89040.18680.01411.3392-0.63081.2762-15.0819-60.9635214.3401
224.054-2.75131.48786.49974.05926.1172-0.219-1.16011.9385-0.45470.551-0.8036-1.916-0.9358-0.28060.9540.01060.08350.8119-0.26520.9627-18.0078-68.2399214.7156
233.49561.3618-1.13974.1848-0.99592.1751-0.3999-1.7410.1818-1.1841-0.6426-0.27480.5702-1.14481.07331.75-0.00280.32451.2563-0.26330.6584-13.7109-76.4848229.5018
241.7685-0.22771.97734.64081.67243.0084-0.2732-0.2430.02140.5135-0.08490.54090.01450.18440.12230.8944-0.23040.13660.6973-0.40320.962312.7272-78.7771216.0076
258.0887-0.27811.97367.71373.81262.4421-0.2252-0.17621.9041-1.16520.29110.0446-1.9190.8514-0.39381.3777-0.12320.21520.5475-0.19450.652713.2986-80.7849197.6754
268.0004-1.2808-0.16453.15393.13333.27630.2509-0.68731.00010.0359-0.2564-0.20980.1611-0.9373-0.16460.7346-0.0390.07390.713-0.09090.39776.7743-85.7239206.5342
276.44666.196-6.5348.7294-7.96847.6516-0.14530.18420.36-1.59890.8405-0.27271.3255-0.2452-0.44190.7171-0.2750.12450.6552-0.03650.353515.9501-91.8698198.9589
281.453-1.0049-0.19082.5244-0.92381.7120.1463-0.2968-0.36620.9448-0.0493-0.08580.1271-1.0139-0.20520.9849-0.3107-0.10461.2072-0.21770.654210.7095-89.9154218.607
294.38660.5854-2.62536.03790.79874.94290.5642-0.533-1.40980.1650.40480.88440.3738-1.1007-0.10551.057-0.3509-0.02451.26360.76731.2964-32.6738-117.3887218.1214
303.1099-0.1547-0.41633.26850.81492.78590.2876-1.1010.42890.39740.15260.1931-0.1304-0.0222-0.41320.62-0.05760.14640.8799-0.01730.4068-13.4004-88.8319212.6769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1001 through 1011 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1012 through 1034 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1035 through 1073 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1074 through 1112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1113 through 1152 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1153 through 1162 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1163 through 1183 )
8X-RAY DIFFRACTION8chain 'A' and (resid 1184 through 1191 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1192 through 1219 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1001 through 1011 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1012 through 1034 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1035 through 1088 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1089 through 1115 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1116 through 1152 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1153 through 1162 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1163 through 1183 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1184 through 1219 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1001 through 1011 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1012 through 1065 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1066 through 1074 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1075 through 1096 )
22X-RAY DIFFRACTION22chain 'C' and (resid 1097 through 1112 )
23X-RAY DIFFRACTION23chain 'C' and (resid 1113 through 1127 )
24X-RAY DIFFRACTION24chain 'C' and (resid 1128 through 1152 )
25X-RAY DIFFRACTION25chain 'C' and (resid 1153 through 1162 )
26X-RAY DIFFRACTION26chain 'C' and (resid 1163 through 1183 )
27X-RAY DIFFRACTION27chain 'C' and (resid 1184 through 1191 )
28X-RAY DIFFRACTION28chain 'C' and (resid 1192 through 1219 )
29X-RAY DIFFRACTION29chain 'D' and (resid 1001 through 1096 )
30X-RAY DIFFRACTION30chain 'D' and (resid 1097 through 1219 )

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