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- PDB-3rf0: Crystal Structure of Exopolyphosphatase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3rf0
TitleCrystal Structure of Exopolyphosphatase from Yersinia pestis
ComponentsExopolyphosphatase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold
Function / homology
Function and homology information


phosphorus metabolic process / polyphosphate catabolic process / exopolyphosphatase / exopolyphosphatase activity / pyrophosphatase activity
Similarity search - Function
Exopolyphosphatase / Pyrophosphatase, GppA/Ppx-type / Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Hypothetical protein af1432 / Hypothetical protein af1432 / ATPase, nucleotide binding domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / NITRATE ION / Exopolyphosphatase / Exopolyphosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Exopolyphosphatase from Yersinia pestis
Authors: Kim, Y. / Zhou, M. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exopolyphosphatase
B: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7495
Polymers49,5792
Non-polymers1703
Water8,395466
1
A: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8983
Polymers24,7901
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8522
Polymers24,7901
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.412, 71.083, 60.195
Angle α, β, γ (deg.)90.00, 118.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exopolyphosphatase / / Putative exopolyphosphatase


Mass: 24789.637 Da / Num. of mol.: 2
Fragment: chymotripsin-treated fragment, C-terminal fragment (UNP resiues 311-519)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: ppx, y1397, YPO2837, YP_2704 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q7CJK2, UniProt: A0A5P8YHM7*PLUS, exopolyphosphatase
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium nitrate, 0.1 M Bis-Tris-Propane pH 7.5, 20 % (v/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41471 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.101 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2086 / Rsym value: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1U6Z

1u6z


Resolution: 1.8→30.191 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2033 5.04 %random
Rwork0.177 ---
all0.179 40375 --
obs0.179 40375 96.95 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.119 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-10.4832 Å20 Å2-6.3566 Å2
2---4.247 Å20 Å2
3----6.2362 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 11 466 3797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113740
X-RAY DIFFRACTIONf_angle_d1.3665113
X-RAY DIFFRACTIONf_dihedral_angle_d15.0071450
X-RAY DIFFRACTIONf_chiral_restr0.106553
X-RAY DIFFRACTIONf_plane_restr0.009681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8001-1.8420.32271410.26512498263996
1.842-1.8880.29781360.23732623275999
1.888-1.93910.28921260.20732604273099
1.9391-1.99610.2781440.20272593273799
1.9961-2.06050.24731260.18982600272699
2.0605-2.13410.24451570.17212566272399
2.1341-2.21960.22791370.17562608274599
2.2196-2.32060.24421260.16962577270399
2.3206-2.44280.22561470.17232585273298
2.4428-2.59580.22591530.17112582273598
2.5958-2.79610.25081300.16932570270098
2.7961-3.07720.22731310.17572544267597
3.0772-3.52190.20971180.16082482260093
3.5219-4.4350.18921300.15342466259692
4.435-30.19510.20821310.18662444257591
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)
12.10370.2491.65321.24490.44241.8925-0.0939-0.36590.08960.1818-0.0096-0.0341-0.2327-0.41160.09390.18510.04320.00320.1365-0.00250.124315.238318.33652.0274
20.1696-0.3131-0.29310.9607-0.42320.879-0.0634-0.0073-0.00370.16220.0250.1007-0.2402-0.0938-0.00590.05320.00070.02620.0596-0.00210.049717.88774.148610.6544
30.10690.26520.09570.7878-0.15450.36550.02640.0798-0.00350.0936-0.033-0.00950.0137-0.0195-0.00410.0544-0.00460.0130.09060.00260.057818.9719.0295-7.1921
40.47490.35670.60651.19130.14990.3332-0.23150.3919-0.1515-0.09650.1376-0.2427-0.00730.19760.01140.06870.00710.00910.11270.01330.091928.95963.3413-1.1877
50.36660.08440.31790.4645-0.13130.9548-0.03750.07450.09710.0733-0.0099-0.0437-0.01350.12120.02820.09260.0002-0.00350.05660.00380.084323.6256-2.14155.5719
60.34640.26810.01840.1846-0.09710.9488-0.01870.0590.1078-0.0091-0.00450.18590.1846-0.2161-0.0380.0812-0.00680.01660.1513-0.01470.18033.9701-3.90315.9174
70.47810.08690.21340.0173-0.01660.4024-0.0162-0.1306-0.1163-0.03110.00860.04070.20570.0434-0.02150.1354-0.00680.0010.1174-0.01380.102520.3776-11.171812.9887
80.3730.07740.18550.1057-0.08820.5510.266-0.0083-0.0199-0.2019-0.1609-0.05590.54880.2282-0.01290.1672-0.1033-0.05710.0061-0.03430.067911.4663-14.07442.2813
90.37730.01420.43080.59910.27920.53310.06870.3966-0.1960.751-0.1913-0.03720.19940.3160.00210.12780.04940.0013-0.1928-0.07440.11716.9587-15.940510.2886
100.7465-0.97530.60392.5333-1.53471.2318-0.19070.20080.17560.54590.1213-0.8317-0.1834-0.14050.10370.1523-0.0196-0.09290.0292-0.040.200519.8169-21.4811-27.194
110.4231-0.25560.05920.62670.54840.5176-0.0133-0.07840.04240.07160.0467-0.09910.07260.009-0.02540.0901-0.002-0.01940.0877-0.00610.08689.0063-15.4874-16.5763
120.312-0.06520.11480.42790.26160.7837-0.06340.03860.0183-0.0396-0.0355-0.0826-0.0370.0070.04670.06260.0087-0.00030.0549-0.01060.06427.1061-22.761-32.1372
130.8464-0.11440.01340.0033-0.05261.01810.11760.1207-0.211-0.1366-0.0780.09760.39420.0756-0.02240.1787-0.0087-0.03140.0555-0.02150.1147-2.1451-26.6205-24.1196
140.7429-0.1817-0.01590.2766-0.47661.5228-0.0161-0.05630.0110.2042-0.0185-0.0718-0.2978-0.10960.01180.0727-0.00240.00870.0418-0.00120.0446-0.8337-8.4856-17.5906
150.5925-0.382-0.22650.5365-0.44641.7674-0.15170.065-0.07230.08310.08240.1671-0.2108-0.47140.00120.07130.0180.01840.1269-0.00550.0902-9.1007-8.2405-20.4206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:22)
2X-RAY DIFFRACTION2chain 'A' and (resseq 23:62)
3X-RAY DIFFRACTION3chain 'A' and (resseq 63:91)
4X-RAY DIFFRACTION4chain 'A' and (resseq 92:121)
5X-RAY DIFFRACTION5chain 'A' and (resseq 122:138)
6X-RAY DIFFRACTION6chain 'A' and (resseq 139:150)
7X-RAY DIFFRACTION7chain 'A' and (resseq 151:164)
8X-RAY DIFFRACTION8chain 'A' and (resseq 165:188)
9X-RAY DIFFRACTION9chain 'A' and (resseq 189:202)
10X-RAY DIFFRACTION10chain 'B' and (resseq 3:22)
11X-RAY DIFFRACTION11chain 'B' and (resseq 23:62)
12X-RAY DIFFRACTION12chain 'B' and (resseq 63:103)
13X-RAY DIFFRACTION13chain 'B' and (resseq 104:121)
14X-RAY DIFFRACTION14chain 'B' and (resseq 122:172)
15X-RAY DIFFRACTION15chain 'B' and (resseq 173:200)

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