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- PDB-3qxg: Crystal structure of pyrophosphatase from bacteroides thetaiotaom... -

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Basic information

Entry
Database: PDB / ID: 3qxg
TitleCrystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation
ComponentsINORGANIC PYROPHOSPHATASE
KeywordsHYDROLASE / PYROPHOSPHATASE / MAGNESIUM BINDING SITE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / ENZYME FUNCTION INITIATIVE / EFI / PSI-2 / Protein Structure Initiative / NYSGXRC
Function / homology
Function and homology information


sugar-phosphatase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...: / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / L(+)-TARTARIC ACID / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsPatskovsky, Y. / Huang, H. / Toro, R. / Gerlt, J.A. / Burley, S.K. / Dunaway-Mariano, D. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2011
Title: Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 Is an Inorganic Pyrophosphatase.
Authors: Huang, H. / Patskovsky, Y. / Toro, R. / Farelli, J.D. / Pandya, C. / Almo, S.C. / Allen, K.N. / Dunaway-Mariano, D.
History
DepositionMar 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Sep 19, 2012Group: Derived calculations
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._audit_author.identifier_ORCID / _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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ptnr2_label_alt_id / _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 1.5Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)54,86117
Polymers54,0162
Non-polymers84515
Water9,458525
1
A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules

A: INORGANIC PYROPHOSPHATASE
B: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,72234
Polymers108,0324
Non-polymers1,69030
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9780 Å2
ΔGint-184 kcal/mol
Surface area35450 Å2
MethodPISA
2
A: INORGANIC PYROPHOSPHATASE
hetero molecules

B: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,86117
Polymers54,0162
Non-polymers84515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3100 Å2
ΔGint-71 kcal/mol
Surface area19070 Å2
MethodPISA
3
A: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5359
Polymers27,0081
Non-polymers5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: INORGANIC PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3268
Polymers27,0081
Non-polymers3187
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.065, 70.586, 76.323
Angle α, β, γ (deg.)90.00, 119.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein INORGANIC PYROPHOSPHATASE


Mass: 27007.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2127 / References: UniProt: Q8A5V9, inorganic diphosphatase

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Non-polymers , 6 types, 540 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 50.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M SODIUM ACETATE, PH 4.5, 0.2M CALCIUM ACETATE, 30% PEG400, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 147352 / % possible obs: 99 % / Observed criterion σ(I): -5 / Redundancy: 3 % / Biso Wilson estimate: 13.32 Å2 / Rsym value: 0.056 / Net I/σ(I): 7.4
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.9 / % possible all: 86

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QU2

3qu2


Resolution: 1.24→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.668 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18203 4418 3 %RANDOM
Rwork0.15241 ---
obs0.1533 142109 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.237 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0.23 Å2
2--0.62 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 43 525 4035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9825181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4545512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15625.316158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13715711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6911510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212864
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.9922338
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.64933791
X-RAY DIFFRACTIONr_scbond_it7.3831459
X-RAY DIFFRACTIONr_scangle_it10.15751354
X-RAY DIFFRACTIONr_rigid_bond_restr2.62813797
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.243→1.275 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 342 -
Rwork0.358 10261 -
obs--97.85 %

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