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- PDB-4ecp: X-ray crystal structure of Inorganic Pyrophosphate PPA from Mycob... -

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Basic information

Entry
Database: PDB / ID: 4ecp
TitleX-ray crystal structure of Inorganic Pyrophosphate PPA from Mycobacterium leprae
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
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 speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray crystal structure of Inorganic Pyrophosphate PPA from Mycobacterium leprae
Authors: Fairman, J.W. / Abendroth, J. / Staker, B.L. / Stewart, L.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)38,1015
Polymers37,9152
Non-polymers1863
Water3,117173
1
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,30315
Polymers113,7446
Non-polymers5599
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area13850 Å2
ΔGint-28 kcal/mol
Surface area39390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.180, 121.180, 66.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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


Mass: 18957.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Gene: ppa, ML0210, MLCB2548.21 / Production host: Escherichia coli (E. coli) / References: UniProt: O69540, inorganic diphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 40% MPD, 100 mM CAPS pH 10.50, 35.04 mg/ml MyleA.01382.a.A1 PW34776, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 33648 / Num. obs: 33514 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.187 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 22.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.4362.255534249899.6
1.85-1.90.3063.025525239399.7
1.9-1.950.2553.955559233098.5
1.95-2.010.1595.75735228599.5
2.01-2.080.1317.595638218098.6
2.08-2.150.1019.96101216099.6
2.15-2.230.08213.776930205399.7
2.23-2.320.07416.87027195898.8
2.32-2.430.05719.997479193999.9
2.43-2.550.05621.977311179799.8
2.55-2.680.0525.0276541752100
2.68-2.850.04628.9682271664100
2.85-3.040.03836.548775154499.9
3.04-3.290.03342.1881191429100
3.29-3.60.02850.867477132399.9
3.6-4.020.02656.5666081192100
4.02-4.650.02361.7959281061100
4.65-5.690.02162.595098894100
5.69-8.050.02261.163977691100
8.050.01967.23209237199.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WCF

1wcf


Resolution: 1.8→34.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.117 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1697 5.1 %RANDOM
Rwork0.1784 ---
all0.1802 33648 --
obs0.1802 33514 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.93 Å2 / Biso mean: 29.377 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-0.5 Å20 Å2
2---1 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 12 173 2742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022682
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9623649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5335332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.87723.529136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89315424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8231521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212111
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 121 -
Rwork0.262 2377 -
all-2498 -
obs--99.56 %
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)
10.9773-0.47570.15251.4953-0.46171.8273-0.0006-0.24960.07820.17510.08960.0219-0.0759-0.2799-0.0890.0432-0.0049-0.02590.1237-0.00160.07949.04638.623610.4808
24.05790.0091-0.84841.70280.01773.3448-0.0002-0.38490.15040.1970.0421-0.0369-0.0436-0.1094-0.04190.0758-0.0248-0.0460.10.00940.08715.4792.009414.3528
30.4551.04360.21248.5706-0.31241.67130.0183-0.25980.10840.3207-0.07490.2526-0.1024-0.08020.05660.0937-0.0055-0.05080.2036-0.0420.1522.99099.632611.5683
41.7497-0.91690.2062.74720.03551.75740.04190.0434-0.0290.0254-0.0674-0.09090.05440.07140.02550.0373-0.0096-0.03040.086-0.01540.100122.45627.28853.6981
511.7145-1.7453-8.01473.79792.971415.37570.0398-1.21250.05550.59-0.0365-0.56320.14970.4737-0.00340.17-0.0348-0.14130.2812-0.00730.131127.46044.047921.7499
60.9593-1.04920.21033.1321-0.04370.55380.12370.23690.0353-0.3539-0.1002-0.21010.19990.0993-0.02340.14590.02430.01580.08150.02030.10187.02078.804-20.2657
72.2316-1.34762.26651.8292-1.75564.27860.15950.26660.1507-0.334-0.0913-0.2090.21140.2803-0.06820.1176-0.00310.02880.05990.010.09868.345515.3962-19.5146
81.54921.03710.42193.6271-0.20221.57690.0620.14420.0299-0.1113-0.0732-0.02420.1176-0.02410.01120.1052-0.0030.00470.06790.04610.08330.236720.4851-16.5713
98.1376-5.30472.34385.1198-2.10311.6103-0.02910.0980.0853-0.0187-0.0028-0.1302-0.0370.19080.03190.0973-0.0168-0.01150.06070.01560.102811.998720.6787-9.118
102.60970.0385-0.37895.1725-0.45624.3545-0.07740.33860.2323-0.6228-0.0792-0.36270.0460.20550.15660.15130.0010.08340.08480.07820.12216.928127.0873-24.7245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 41
2X-RAY DIFFRACTION2A42 - 76
3X-RAY DIFFRACTION3A77 - 97
4X-RAY DIFFRACTION4A98 - 141
5X-RAY DIFFRACTION5A142 - 158
6X-RAY DIFFRACTION6B1 - 31
7X-RAY DIFFRACTION7B32 - 60
8X-RAY DIFFRACTION8B61 - 108
9X-RAY DIFFRACTION9B109 - 133
10X-RAY DIFFRACTION10B134 - 159

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