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- PDB-6k27: Pyrophosphatase with PPi from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 6k27
TitlePyrophosphatase with PPi from Acinetobacter baumannii
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / Pyrophosphatase with PPi from Acinetobacter baumannii
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
DIPHOSPHATE / Inorganic pyrophosphatase / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsSu, J.
CitationJournal: Int J Mol Sci / Year: 2019
Title: Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate.
Authors: Si, Y. / Wang, X. / Yang, G. / Yang, T. / Li, Y. / Ayala, G.J. / Li, X. / Wang, H. / Su, J.
History
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_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
G: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,00040
Polymers156,0258
Non-polymers1,97532
Water0
1
A: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
hetero molecules

A: Inorganic pyrophosphatase
F: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,50030
Polymers117,0196
Non-polymers1,48124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14330 Å2
ΔGint-236 kcal/mol
Surface area39270 Å2
MethodPISA
2
B: Inorganic pyrophosphatase
hetero molecules

B: Inorganic pyrophosphatase
hetero molecules

B: Inorganic pyrophosphatase
hetero molecules

E: Inorganic pyrophosphatase
hetero molecules

E: Inorganic pyrophosphatase
hetero molecules

E: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,50030
Polymers117,0196
Non-polymers1,48124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation4_445x-1/3,y-2/3,z+1/31
crystal symmetry operation5_545-y+2/3,x-y-2/3,z+1/31
crystal symmetry operation6_555-x+y+2/3,-x+1/3,z+1/31
Buried area14200 Å2
ΔGint-238 kcal/mol
Surface area39530 Å2
MethodPISA
3
C: Inorganic pyrophosphatase
G: Inorganic pyrophosphatase
hetero molecules

C: Inorganic pyrophosphatase
G: Inorganic pyrophosphatase
hetero molecules

C: Inorganic pyrophosphatase
G: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,50030
Polymers117,0196
Non-polymers1,48124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area14390 Å2
ΔGint-237 kcal/mol
Surface area38480 Å2
MethodPISA
4
D: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase
hetero molecules

D: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase
hetero molecules

D: Inorganic pyrophosphatase
H: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,50030
Polymers117,0196
Non-polymers1,48124
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area14380 Å2
ΔGint-233 kcal/mol
Surface area38530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.294, 110.294, 302.492
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 19503.141 Da / Num. of mol.: 8 / Mutation: A139S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ppa / Production host: Escherichia coli (E. coli)
References: UniProt: N9S5K0, UniProt: A0A333SMX2*PLUS, inorganic diphosphatase
#2: Chemical
ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Source detailsThe protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference ...The protein was from a strain of Acinetobacter baumannii from a hospital. The sequence reference used is from a different species Acinetobacter ursingii NIPH 706.

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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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.86→19.763 Å / Num. obs: 114729 / % possible obs: 99.5 % / Redundancy: 5 % / Net I/σ(I): 8.4
Reflection shellResolution: 1.86→1.89 Å / Num. unique obs: 5740

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Processing

SoftwareName: PHENIX / Version: 1.12_2829 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→19.763 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.7
RfactorNum. reflection% reflection
Rfree0.2455 1998 1.74 %
Rwork0.1955 --
obs0.1964 114589 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.12 Å2 / Biso mean: 34.6801 Å2 / Biso min: 18.17 Å2
Refinement stepCycle: final / Resolution: 1.86→19.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10731 0 96 0 10827
Biso mean--44.3 --
Num. residues----1384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711080
X-RAY DIFFRACTIONf_angle_d0.84615136
X-RAY DIFFRACTIONf_chiral_restr0.061656
X-RAY DIFFRACTIONf_plane_restr0.0061968
X-RAY DIFFRACTIONf_dihedral_angle_d5.5146688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.90650.35241390.299881128251100
1.9065-1.9580.31061430.264780778220100
1.958-2.01550.30811420.249480248166100
2.0155-2.08050.24471430.239781258268100
2.0805-2.15480.20921460.224880348180100
2.1548-2.2410.28121440.217680718215100
2.241-2.34280.30951400.223480818221100
2.3428-2.46610.28891420.222380448186100
2.4661-2.62030.29451420.229681048246100
2.6203-2.82210.23051430.216780728215100
2.8221-3.10510.25051470.206280558202100
3.1051-3.55210.23021440.180780958239100
3.5521-4.46680.21041470.15018016816399
4.4668-19.76460.21771360.1627681781795

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