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- PDB-5j16: Crystal structure of Inositol monophosphate bound SaIMPase-II -

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Basic information

Entry
Database: PDB / ID: 5j16
TitleCrystal structure of Inositol monophosphate bound SaIMPase-II
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / inositol monophosphatase / sugar phosphatase fold / substrate bound complex / SuhB
Function / homology
Function and homology information


Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / D-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1-PHOSPHATE / PHOSPHATE ION / Inositol monophosphatase family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsDutta, A. / Bhattacharyya, S. / Das, A.K.
CitationJournal: To Be Published
Title: Crystal structure of Inositol monophosphate bound SaIMPase-II
Authors: Dutta, A. / Bhattacharyya, S. / Das, A.K.
History
DepositionMar 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: Inositol monophosphatase family protein
B: Inositol monophosphatase family protein
C: Inositol monophosphatase family protein
D: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,03116
Polymers125,8414
Non-polymers1,19012
Water3,225179
1
A: Inositol monophosphatase family protein
D: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4348
Polymers62,9212
Non-polymers5136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol monophosphatase family protein
C: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5978
Polymers62,9212
Non-polymers6776
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.942, 78.762, 80.052
Angle α, β, γ (deg.)105.460, 102.280, 109.470
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Inositol monophosphatase family protein / Inositol monophosphatase-II


Mass: 31460.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MSSA476) (bacteria)
Strain: MSSA476 / Gene: SAS1042 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A1I9GET0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IPD / D-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H11O9P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M CaCl2, 0.1M Bis-Tris pH 6.0, 18-22% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.399→72.787 Å / Num. all: 43376 / Num. obs: 43376 / % possible obs: 96.3 % / Redundancy: 4 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.069 / Rsym value: 0.06 / Net I/av σ(I): 12.4 / Net I/σ(I): 18.1 / Num. measured all: 172821
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.533.90.38322428461530.2220.4430.3833.493.3
2.53-2.6840.2812.82355359000.1620.3240.2814.695.3
2.68-2.8740.19642255456470.1130.2260.1966.695.8
2.87-3.140.12962094852500.0740.1480.1299.796.3
3.1-3.3940.0799.71924148200.0460.0920.07915.496.9
3.39-3.7940.04516.71771744400.0260.0520.04525.697.5
3.79-4.3840.032231563939210.0180.0370.03234.898.1
4.38-5.3640.02428.71325033180.0140.0280.02443.298.6
5.36-7.5840.02924.81028525790.0170.0330.02938.699.1
7.58-19.74640.01835.9535013480.010.0210.0186294

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.57 Å19.75 Å
Translation2.57 Å19.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.16data scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T0J

3t0j


Resolution: 2.4→72.79 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2095 / WRfactor Rwork: 0.163 / FOM work R set: 0.8254 / SU B: 8.624 / SU ML: 0.196 / SU R Cruickshank DPI: 0.4155 / SU Rfree: 0.2581 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.416 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 2196 5.1 %RANDOM
Rwork0.1809 ---
obs0.1837 41180 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.92 Å2 / Biso mean: 38.021 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å2-0.42 Å2-0.44 Å2
2---1.27 Å2-0.19 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 2.4→72.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7740 0 61 179 7980
Biso mean--38.38 32.68 -
Num. residues----1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197960
X-RAY DIFFRACTIONr_bond_other_d0.0020.027416
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.96110848
X-RAY DIFFRACTIONr_angle_other_deg1.0633.00217002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96851010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95225.237359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.456151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1321529
X-RAY DIFFRACTIONr_chiral_restr0.1050.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219181
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021804
LS refinement shellResolution: 2.399→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 150 -
Rwork0.248 2862 -
all-3012 -
obs--91.61 %

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