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- PDB-4xel: Crystal structure of Inorganic pyrophosphatase (PPase) from Pseud... -

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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

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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
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

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Components

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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

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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 / Polyethylene glycol


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


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 / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 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

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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: 0

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

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Phasing

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

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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

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