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- PDB-5tea: Crystal structure of an inorganic pyrophosphatase from Neisseria ... -

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Basic information

Entry
Database: PDB / ID: 5tea
TitleCrystal structure of an inorganic pyrophosphatase from Neisseria gonorrhoeae
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / structural genomics / SSGCID / NIAID / gonococci / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytosol
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of an inorganic pyrophosphatase from
Authors: Edwards, T.E. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
D: Inorganic pyrophosphatase
E: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,41719
Polymers124,9296
Non-polymers48913
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-82 kcal/mol
Surface area37450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.720, 65.650, 133.210
Angle α, β, γ (deg.)90.000, 115.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-419-

HOH

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Components

#1: Protein
Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 20821.441 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: ppa / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K0G4, inorganic diphosphatase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 45.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: NegoA.01623.a.B1.PS37944 at 32.6 mg/mL against JCSG A4, 0.2M CaCl2, 0.1 M NaOAc pH 4.6, 30% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 94722 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.79
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.85-1.90.5592.440.806199.9
1.9-1.950.4483.010.874199.7
1.95-2.010.3463.810.906199.7
2.01-2.070.2684.690.94199.6
2.07-2.140.2175.640.956199.5
2.14-2.210.1776.720.966199.6
2.21-2.290.1567.460.97199.6
2.29-2.390.1368.180.977199.5
2.39-2.490.129.080.98199.7
2.49-2.620.1089.940.981199.6
2.62-2.760.09911.110.984199.7
2.76-2.930.08812.20.987199.6
2.93-3.130.08213.260.987199.5
3.13-3.380.07714.120.988199.5
3.38-3.70.07114.840.989199.5
3.7-4.140.06615.540.992199.2
4.14-4.780.06116.230.993199.6
4.78-5.850.05616.330.994199.5
5.85-8.270.05116.270.995199.6
8.27-500.04216.130.996195.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2499refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I98
Resolution: 1.85→40.029 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.35
RfactorNum. reflection% reflection
Rfree0.2089 2041 2.16 %
Rwork0.1695 --
obs0.1704 94708 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.33 Å2 / Biso mean: 31.5184 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: final / Resolution: 1.85→40.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8047 0 13 749 8809
Biso mean--38.85 37 -
Num. residues----1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068283
X-RAY DIFFRACTIONf_angle_d0.77111286
X-RAY DIFFRACTIONf_chiral_restr0.0571278
X-RAY DIFFRACTIONf_plane_restr0.0051496
X-RAY DIFFRACTIONf_dihedral_angle_d13.3024972
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8930.36121460.267861206266100
1.893-1.94040.30321320.230861796311100
1.9404-1.99280.23291470.211461586305100
1.9928-2.05150.24371220.200561526274100
2.0515-2.11770.23481180.193561606278100
2.1177-2.19340.23751420.184861346276100
2.1934-2.28120.21681450.177661236268100
2.2812-2.3850.23071340.180561816315100
2.385-2.51070.23531200.180961756295100
2.5107-2.6680.23061520.176861416293100
2.668-2.87390.21251420.175461696311100
2.8739-3.1630.22111440.172762026346100
3.163-3.62050.21151230.158461926315100
3.6205-4.56040.14851460.133762296375100
4.5604-40.0380.1811280.15276352648099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.93790.3572-0.23573.87710.48563.52430.2338-0.5107-0.28930.0857-0.2131.2994-0.0001-0.9498-0.08340.4002-0.1722-0.0360.55220.02290.4007-19.3919-5.055343.7522
21.22690.96270.37372.7240.12131.17420.0747-0.0840.14030.1971-0.01190.334-0.0506-0.318-0.0390.2335-0.00440.04080.27150.03940.1878-8.284110.311945.924
31.6121-0.07451.12882.6147-0.50630.85470.0532-0.2598-0.01440.28070.06770.2395-0.1114-0.315-0.16980.2098-0.0290.01990.2680.02120.153-8.52162.466745.5422
41.1486-0.09580.99161.3678-0.56093.9664-0.0191-0.0844-0.13930.06510.05670.07850.4272-0.3436-0.0270.2401-0.07420.01230.19410.04220.1878-4.2423-5.635243.7877
52.12351.3378-0.51933.2119-0.10934.1266-0.0321-0.2575-0.07530.2617-0.00620.03220.08190.10570.0440.17610.0049-0.01730.1870.0420.14534.85982.100253.805
67.8035-4.28320.22988.4451-1.19133.5538-0.0268-0.6314-0.14060.2020.17130.28970.1343-0.5829-0.0620.3411-0.13630.00650.40820.09490.2369-15.6402-7.89853.975
73.2715-1.7675.4226.9272-2.9499.1745-0.13310.0091-0.04660.1692-0.0685-0.9440.42061.15880.09350.24980.03620.02290.5273-0.03150.359124.863122.56746.5675
80.73660.1119-0.19540.36770.73514.06140.1915-0.1050.11450.01930.0228-0.1464-0.3960.5191-0.21890.2104-0.06030.01450.1828-0.00720.179617.770926.9222.9706
93.1283-0.9895-0.46671.6096-0.22953.6720.1027-0.09410.24320.1510.0245-0.1594-0.40330.3354-0.0920.191-0.0441-0.00830.1512-0.03460.140415.613326.186315.3344
100.8103-0.1569-0.00132.42351.10172.0636-0.02230.0154-0.00390.01810.1152-0.1225-0.14390.0342-0.10160.1423-0.010.01820.14560.01150.10929.776526.35848.4166
111.7061.1881-1.20514.50720.51216.30660.1761-0.08770.16170.3968-0.13360.0704-0.54160.0821-0.00120.23640.01990.03140.14930.01210.15285.102937.755217.2655
129.0323-0.01653.77836.4835-0.76254.12040.22980.49790.5775-0.2555-0.018-0.4989-0.57670.6822-0.06870.2823-0.11030.0970.2895-0.0190.203622.022633.54323.0848
137.2847-1.63730.21871.2762.03565.2209-0.00250.41450.5201-0.2151-0.0683-0.6735-0.35370.84550.1890.2455-0.0149-0.03940.4432-0.01960.440732.0716-1.091623.6398
142.2987-1.04441.6671.8191-1.47552.34970.04010.2350.0676-0.1032-0.1072-0.2225-0.06720.28510.09770.1979-0.00060.01210.1801-0.02640.211417.53597.072316.4597
155.6657-2.1671-1.32054.4117-0.11533.59170.08520.7186-0.1775-0.6151-0.2324-0.3130.07450.29210.17080.26230.0010.02450.2526-0.03440.210521.8167-0.963816.1912
162.0354-0.01630.75974.98871.97094.94150.01660.1691-0.0603-0.1853-0.0245-0.13790.03030.1339-0.00650.1126-0.00350.01510.1356-0.00030.153117.8811-3.20121.6733
171.3331-0.30021.50591.42680.15445.05680.19840.0041-0.0643-0.0965-0.05710.02050.578-0.0731-0.16170.198-0.00850.02190.12270.00120.18789.3284-6.022522.3738
183.36771.35850.94274.2547-0.82271.7770.09790.3971-0.6151-0.2283-0.038-0.65990.22320.4913-0.03640.27570.08370.04150.2678-0.08860.234324.6906-11.034415.6475
193.53260.78462.62993.63870.21122.69310.2127-0.4244-0.37190.9377-0.03250.9797-0.0466-0.9791-0.31020.40680.10490.10390.73190.06810.5398-27.974615.361821.8277
201.6444-1.27440.10542.2229-0.89812.18590.0589-0.0177-0.17770.16810.09110.40850.1387-0.458-0.06260.1766-0.07660.01810.2820.01110.2057-15.06616.752523.7788
211.111-0.4783-0.23432.43950.82482.33710.06530.1712-0.1658-0.0805-0.0810.26240.0099-0.30980.01850.1031-0.0112-0.02840.30930.00190.216-14.98413.770312.8754
222.8133-1.52120.21132.52210.34961.76390.11150.2271-0.3415-0.1405-0.1920.54320.3678-0.6075-0.02580.1724-0.1131-0.04890.3847-0.03950.249-15.78492.762911.5321
233.18991.7814-0.22685.02930.15662.20730.02840.0821-0.1881-0.15230.0888-0.9237-0.34360.4325-0.08090.1739-0.0610.00620.2496-0.03410.26327.539522.87536.0959
243.34972.14131.28241.46220.67420.7348-0.1906-0.1825-0.18390.02370.2176-0.80150.41150.45050.1120.18650.0224-0.00270.3328-0.05830.417728.876110.213133.422
251.65030.4792-1.613.1594-1.0723.05370.0231-0.2748-0.1630.1807-0.0336-0.30240.07810.4337-0.03210.1191-0.0143-0.03830.2275-0.01990.155319.78185.744938.0228
262.82621.5042-1.38724.52970.58834.5213-0.0401-0.1889-0.23630.10690.0471-0.43430.08710.37070.02170.1369-0.0246-0.01330.1874-0.02180.171223.978418.44739.2515
271.24080.34460.06052.1402-0.71712.37020.0617-0.1492-0.07280.1727-0.053-0.2502-0.25130.29910.00460.2225-0.088-0.0260.2574-0.03460.194821.020425.446144.6762
282.17930.28540.47036.2673-0.68952.32750.1036-0.2689-0.11150.3549-0.0507-0.1718-0.03020.2983-0.05430.2414-0.0421-0.02060.269-0.00710.11617.591512.814752.8123
296.6641-2.1253-2.90193.26660.73524.07430.1117-0.7363-0.14740.25690.0293-0.8214-0.37361.1107-0.07730.2359-0.1557-0.09370.5592-0.0420.466235.822524.540546.5741
301.8092-0.397-0.98441.79581.30414.48850.0466-0.0506-0.07040.41760.01110.47250.044-0.8481-0.02410.28130.03210.12330.30570.06790.2749-15.552825.325444.0383
313.11062.1718-0.82372.1486-0.80384.08370.1541-0.0820.13950.15470.08380.4233-0.1101-0.5768-0.28850.19250.050.04380.29050.0410.319-15.620424.88128.5545
323.8846-0.4383-0.60943.19731.37631.25130.11660.56120.4986-0.16690.08610.559-0.5347-0.9608-0.18220.32260.13210.04950.4940.12040.3207-15.802530.681537.8955
331.31331.1264-0.42646.9114-1.10973.68910.1225-0.11260.08340.23670.05790.1648-0.3331-0.1853-0.18080.19380.04980.06310.21350.01120.1608-8.497828.603241.6279
342.4592-0.972-0.76673.9586-1.2432.23570.095-0.0660.24160.24220.12440.0943-0.5191-0.1019-0.18150.30530.0270.0870.2051-0.02050.1756-3.984631.451546.0183
350.82130.45020.66671.56890.93585.1930.07240.050.18750.236-0.03530.1096-0.8014-0.2568-0.01920.38860.06220.1020.21290.00920.231-4.532439.721931.1632
366.0660.2408-1.36674.71571.66663.26460.25950.02220.50270.269-0.05831.1226-0.7439-0.7359-0.08590.51490.23340.25060.46020.09520.4997-20.959737.368147.0814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 16 )A4 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 51 )A17 - 51
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 85 )A52 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 128 )A86 - 128
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 158 )A129 - 158
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 176 )A159 - 176
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 16 )B3 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 51 )B17 - 51
9X-RAY DIFFRACTION9chain 'B' and (resid 52 through 85 )B52 - 85
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 128 )B86 - 128
11X-RAY DIFFRACTION11chain 'B' and (resid 129 through 158 )B129 - 158
12X-RAY DIFFRACTION12chain 'B' and (resid 159 through 176 )B159 - 176
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 16 )C3 - 16
14X-RAY DIFFRACTION14chain 'C' and (resid 17 through 51 )C17 - 51
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 71 )C52 - 71
16X-RAY DIFFRACTION16chain 'C' and (resid 72 through 111 )C72 - 111
17X-RAY DIFFRACTION17chain 'C' and (resid 112 through 150 )C112 - 150
18X-RAY DIFFRACTION18chain 'C' and (resid 151 through 176 )C151 - 176
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 16 )D3 - 16
20X-RAY DIFFRACTION20chain 'D' and (resid 17 through 85 )D17 - 85
21X-RAY DIFFRACTION21chain 'D' and (resid 86 through 128 )D86 - 128
22X-RAY DIFFRACTION22chain 'D' and (resid 129 through 176 )D129 - 176
23X-RAY DIFFRACTION23chain 'E' and (resid 3 through 29 )E3 - 29
24X-RAY DIFFRACTION24chain 'E' and (resid 30 through 39 )E30 - 39
25X-RAY DIFFRACTION25chain 'E' and (resid 40 through 51 )E40 - 51
26X-RAY DIFFRACTION26chain 'E' and (resid 52 through 85 )E52 - 85
27X-RAY DIFFRACTION27chain 'E' and (resid 86 through 128 )E86 - 128
28X-RAY DIFFRACTION28chain 'E' and (resid 129 through 158 )E129 - 158
29X-RAY DIFFRACTION29chain 'E' and (resid 159 through 175 )E159 - 175
30X-RAY DIFFRACTION30chain 'F' and (resid 3 through 29 )F3 - 29
31X-RAY DIFFRACTION31chain 'F' and (resid 30 through 51 )F30 - 51
32X-RAY DIFFRACTION32chain 'F' and (resid 52 through 71 )F52 - 71
33X-RAY DIFFRACTION33chain 'F' and (resid 72 through 99 )F72 - 99
34X-RAY DIFFRACTION34chain 'F' and (resid 100 through 128 )F100 - 128
35X-RAY DIFFRACTION35chain 'F' and (resid 129 through 158 )F129 - 158
36X-RAY DIFFRACTION36chain 'F' and (resid 159 through 176 )F159 - 176

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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