[English] 日本語
Yorodumi
- PDB-4xel: Crystal structure of Inorganic pyrophosphatase (PPase) from Pseud... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xel
TitleCrystal structure of Inorganic pyrophosphatase (PPase) from Pseudomonas aeruginosa
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / SSGCID / Pseudomonas aeruginosa / Inorganic pyrophosphatase / Structural Genomics / 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 / extracellular space / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Inorganic pyrophosphatase (PPase) from Pseudomonas aeruginosa
Authors: Abendroth, J. / Sullivan, A.H. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.2Sep 27, 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_struct_conn_angle / 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 / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6139
Polymers40,9012
Non-polymers7127
Water3,423190
1
A: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,23915
Polymers61,3513
Non-polymers1,88812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5730 Å2
ΔGint-151 kcal/mol
Surface area21070 Å2
MethodPISA
2
B: Inorganic pyrophosphatase
hetero molecules

B: Inorganic pyrophosphatase
hetero molecules

B: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,59912
Polymers61,3513
Non-polymers2489
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area6510 Å2
ΔGint-159 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.360, 82.360, 125.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Detailsbiological unit is a trimer generatred from monomer A by the operations: x,y,z and -x+y,-x+1,z and -y+1,x-y+1,z, and from monomer B by the operations: x,y,z and -y+2,x-y+1,z and -x+y+1,-x+2,z

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 20450.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: ppa, PA4031 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HWZ6, inorganic diphosphatase

-
Non-polymers , 5 types, 197 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Microlytics , MCSG1 F4: 200mM MgCl2, 100mM NaCitrate/Citric acid pH 5.5, 40% PEG 400; PsaeA.00023.a.B1.PS02168 at 20mg/ml; cryo: 25% in two steps; tray 258340c5, puck ymq0-4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 17, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32180 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 35.29 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.059 / Χ2: 0.998 / Net I/σ(I): 14.53 / Num. measured all: 122971
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.7850.482.559099238623820.55799.8
2.05-2.110.8270.3813.228870233423300.44299.8
2.11-2.170.9070.2824.278677227922780.327100
2.17-2.240.9350.225.318496220722050.25599.9
2.24-2.310.9480.1916.138063212321130.22199.5
2.31-2.390.9740.1527.457846206020530.17699.7
2.39-2.480.9810.1259.237662199819940.14499.8
2.48-2.580.9850.10810.657388193419250.12499.5
2.58-2.70.9910.08712.847080185218450.199.6
2.7-2.830.9930.07115.76817178117680.08299.3
2.83-2.980.9940.05919.336275165316380.06899.1
2.98-3.160.9960.04923.076016160015840.05799
3.16-3.380.9960.04626.195616148214630.05298.7
3.38-3.650.9970.0428.675233141213830.04697.9
3.65-40.9970.03730.744715127312440.04297.7
4-4.470.9970.03632.094303116611370.04197.5
4.47-5.160.9980.03332.713838103410100.03897.7
5.16-6.320.9980.02932.7332568708430.03396.9
6.32-8.940.9980.02733.4525166826500.03195.3
8.940.9970.02932.2712053863350.03386.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å47.05 Å
Translation2 Å47.05 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALE2.5.6data scaling
PHASERphasing
ARPmodel building
Cootmodel building
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3i41, truncated

3i41


Resolution: 2→36.025 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1586 4.93 %Random selection
Rwork0.22 30554 --
obs0.2222 32140 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.88 Å2 / Biso mean: 45.0675 Å2 / Biso min: 22.09 Å2
Refinement stepCycle: final / Resolution: 2→36.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 25 190 2795
Biso mean--50.55 44.42 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082673
X-RAY DIFFRACTIONf_angle_d13661
X-RAY DIFFRACTIONf_chiral_restr0.043417
X-RAY DIFFRACTIONf_plane_restr0.006481
X-RAY DIFFRACTIONf_dihedral_angle_d12.073943
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.06460.36551290.27927882917100
2.0646-2.13840.29681470.258327772924100
2.1384-2.2240.28471690.247527982967100
2.224-2.32520.32711540.242127572911100
2.3252-2.44780.27221340.231428112945100
2.4478-2.60110.30891380.237927932931100
2.6011-2.80180.33781430.236127962939100
2.8018-3.08370.28731210.23672788290999
3.0837-3.52950.25851540.2172766292099
3.5295-4.44550.25271610.19662734289598
4.4455-36.03060.20961360.20352746288296
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)
16.142-0.17790.75496.7781-1.06823.0882-0.03830.57630.3028-1.19260.08690.22540.15820.7982-0.04480.6836-0.17570.17390.6439-0.03380.311618.248455.136532.3216
22.46661.69031.09814.1476-0.08860.6309-0.1140.4663-0.2054-0.61750.3019-0.08320.00460.3953-0.18710.40630.00990.04240.3907-0.05120.29488.996740.307340.2626
31.18081.4268-0.53194.7264-1.91993.11630.26710.229-0.212-0.5726-0.0761-0.22860.20890.7135-0.15680.33650.05140.03060.4075-0.07730.307115.698541.952541.9784
43.77870.12130.58311.13780.6542.6791-0.05420.4234-0.4255-0.22430.0794-0.25890.040.3266-0.03070.2477-0.01940.07440.3885-0.01320.338918.986147.87743.7093
55.4325-0.31941.36283.14670.1293.5738-0.26520.1350.0737-0.03690.1229-0.093-0.36030.48220.19370.4181-0.18840.04280.3869-0.01190.42321.290761.595448.0386
62.37761.95720.87583.76590.91932.20840.20850.1234-0.5361-0.0266-0.1465-0.65680.4880.4945-0.16230.31560.05920.02520.3944-0.01010.489822.103739.897750.9965
75.081-0.56733.44622.1937-2.043.66140.2730.6353-0.589-0.8070.2619-0.42580.37091.44460.99260.5636-0.04540.48570.7515-0.10960.60227.712948.374933.3222
81.184-2.2848-0.31974.9485-0.30113.0969-0.3493-0.34160.3380.86980.2324-0.0565-0.14080.22780.17250.5714-0.11020.03750.5860.06730.343325.22259.225785.8311
94.2601-0.0942-1.04892.4719-0.11340.25440.1846-0.8741-0.15370.3698-0.0289-0.0381-0.10470.2352-0.16270.2649-0.0375-0.00930.42320.06570.220840.454860.558977.9489
106.43860.5858-1.25632.6419-0.58210.6221-0.0441-0.176-0.35720.11110.104-0.16050.11250.1824-0.08450.25210.0022-0.00030.30940.03420.277444.111757.817672.1356
111.48340.6956-1.73841.09560.51664.3817-0.1331-0.3932-0.23150.3202-0.2661-0.3480.49540.44180.18020.3788-0.04910.02290.38530.06520.32933.534557.777878.3704
124.71371.2208-0.08912.81670.34182.86660.0425-0.2135-0.4750.2231-0.1191-0.09420.5059-0.1844-0.01080.3792-0.07380.05060.3980.10440.372726.692254.00773.5728
137.20051.78671.29972.65380.55414.0995-0.20740.3288-0.75040.17310.2672-0.06090.6716-0.0411-0.03120.3608-0.03780.02760.2594-0.01030.365632.173450.672263.632
141.52720.2641-0.07122.1918-2.20913.47980.1179-0.1934-0.39270.45170.27110.07070.3218-0.0204-0.2550.4099-0.0197-0.03870.33730.04530.49233.871246.77778.1752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 45 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 69 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 110 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 123 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 158 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 175 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 15 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 38 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 58 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 59 through 84 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 85 through 123 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 124 through 139 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 175 )B0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more