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- PDB-5h4f: Structure of inorganic pyrophosphatase crystallised as a contaminant -

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Basic information

Entry
Database: PDB / ID: 5h4f
TitleStructure of inorganic pyrophosphatase crystallised as a contaminant
Componentsinorganic pyrophosphatase
KeywordsHYDROLASE / inorganic pyrophosphatase / contamination / bacterial / MarathonMR
Function / homologyInorganic Pyrophosphatase / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChaudhary, S. / Hatti, K. / Srinivasan, N. / Murthy, M.R.N. / Sekar, K.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structure determination of contaminant proteins using the MarathonMR procedure.
Authors: Hatti, K. / Biswas, A. / Chaudhary, S. / Dadireddy, V. / Sekar, K. / Srinivasan, N. / Murthy, M.R.
History
DepositionOct 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Nov 8, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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

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Assembly

Deposited unit
A: inorganic pyrophosphatase
B: inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3014
Polymers39,1712
Non-polymers1312
Water2,432135
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)117,90412
Polymers117,5126
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area13990 Å2
ΔGint-276 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.098, 108.098, 155.607
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein inorganic pyrophosphatase


Mass: 19585.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: inorganic diphosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→29.5 Å / Num. obs: 22181 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IPW

1ipw


Resolution: 2.05→29.5 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.777 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.193 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1128 5.1 %RANDOM
Rwork0.2114 ---
obs0.21349 21048 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.385 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.23 Å20 Å2
2--0.45 Å20 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.05→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 2 135 2849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192782
X-RAY DIFFRACTIONr_bond_other_d0.0020.022612
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9723789
X-RAY DIFFRACTIONr_angle_other_deg0.91636056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59425.36125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21415451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.569158
X-RAY DIFFRACTIONr_chiral_restr0.080.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213119
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02573
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_it1.5972.8451386
X-RAY DIFFRACTIONr_mcbond_other1.5932.8441385
X-RAY DIFFRACTIONr_mcangle_it2.584.2571729
X-RAY DIFFRACTIONr_mcangle_other2.584.2571730
X-RAY DIFFRACTIONr_scbond_it1.7573.0441395
X-RAY DIFFRACTIONr_scbond_other1.7573.0451396
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8794.4572061
X-RAY DIFFRACTIONr_long_range_B_refined4.54133.4693042
X-RAY DIFFRACTIONr_long_range_B_other4.5433.4743043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 87 -
Rwork0.277 1525 -
obs--100 %

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