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- PDB-4rpa: Crystal structure of inorganic pyrophosphatase from Staphylococcu... -

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Basic information

Entry
Database: PDB / ID: 4rpa
TitleCrystal structure of inorganic pyrophosphatase from Staphylococcus aureus in complex with Mn2+
ComponentsProbable manganese-dependent inorganic pyrophosphatase
KeywordsHYDROLASE / mixed alpha/beta fold / inorganic pyrophosphatase
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / manganese ion binding / cytoplasm
Similarity search - Function
Manganese-dependent inorganic pyrophosphatase, probable / DHHA2 domain / DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain ...Manganese-dependent inorganic pyrophosphatase, probable / DHHA2 domain / DHHA2 domain / DHHA2 domain superfamily / DHHA2 domain / DHHA2 / inorganic pyrophosphatase (n-terminal core) / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / : / Probable manganese-dependent inorganic pyrophosphatase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGajadeera, C.S. / Tsodikov, O.V.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.
Authors: Gajadeera, C.S. / Zhang, X. / Wei, Y. / Tsodikov, O.V.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Sep 20, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Probable manganese-dependent inorganic pyrophosphatase
B: Probable manganese-dependent inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7026
Polymers70,4822
Non-polymers2204
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-32 kcal/mol
Surface area24410 Å2
MethodPISA
2
A: Probable manganese-dependent inorganic pyrophosphatase
B: Probable manganese-dependent inorganic pyrophosphatase
hetero molecules

A: Probable manganese-dependent inorganic pyrophosphatase
B: Probable manganese-dependent inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,40312
Polymers140,9644
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area7460 Å2
ΔGint-80 kcal/mol
Surface area46450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.406, 99.406, 425.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Probable manganese-dependent inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase


Mass: 35240.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ppaC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D9RMT1, UniProt: P65752*PLUS, inorganic diphosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.32 M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 74109 / Num. obs: 74109 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1K23, each domain individually, sequentially

1k23


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.696 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24922 3695 5 %RANDOM
Rwork0.22037 ---
obs0.22181 70192 99.93 %-
all-70192 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.892 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.52 Å20 Å2
2--1.03 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 4 365 5129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194845
X-RAY DIFFRACTIONr_bond_other_d0.0010.024666
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.9756530
X-RAY DIFFRACTIONr_angle_other_deg0.711310772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.395614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60225.926216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97915872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.091518
X-RAY DIFFRACTIONr_chiral_restr0.0610.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1373.7912462
X-RAY DIFFRACTIONr_mcbond_other1.1373.792461
X-RAY DIFFRACTIONr_mcangle_it1.975.6793074
X-RAY DIFFRACTIONr_mcangle_other1.975.683075
X-RAY DIFFRACTIONr_scbond_it1.3343.9572383
X-RAY DIFFRACTIONr_scbond_other1.3313.962380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2515.8713457
X-RAY DIFFRACTIONr_long_range_B_refined4.65330.515688
X-RAY DIFFRACTIONr_long_range_B_other4.40230.2075558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 255 -
Rwork0.295 5103 -
obs--100 %

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