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- PDB-5f24: Crystal structure of dual specific IMPase/NADP phosphatase bound ... -

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Basic information

Entry
Database: PDB / ID: 5f24
TitleCrystal structure of dual specific IMPase/NADP phosphatase bound with D-inositol-1-phosphate
ComponentsInositol monophosphatase
KeywordsHYDROLASE / IMPase/NADP phosphatase / substrate bound complex / FIG superfamily / phosphatase
Function / homology
Function and homology information


inositol monophosphate 1-phosphatase activity / inositol metabolic process / nucleotide binding / signal transduction / metal ion binding
Similarity search - Function
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 / : / Inositol monophosphatase family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBhattacharyya, S. / Dutta, D. / Ghosh, A.K. / Das, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and Technology India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural elucidation of the NADP(H) phosphatase activity of staphylococcal dual-specific IMPase/NADP(H) phosphatase
Authors: Bhattacharyya, S. / Dutta, A. / Dutta, D. / Ghosh, A.K. / Das, A.K.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 23, 2015ID: 4G60
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 25, 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol monophosphatase
B: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,43416
Polymers60,8422
Non-polymers1,59214
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-64 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.567, 67.835, 137.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-404-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 4 - 264 / Label seq-ID: 4 - 264

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inositol monophosphatase / IMPase/NADP phosphatase / Myo-inositol-1(Or 4)-monophosphatase


Mass: 30421.021 Da / Num. of mol.: 2 / Mutation: I142F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli M15 (bacteria) / Strain (production host): M15
References: UniProt: A0A0D6HL44, UniProt: Q2FVV7*PLUS, inositol-phosphate phosphatase

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Non-polymers , 7 types, 246 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IPD / D-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O9P
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M CACL2 2H20, 0.1M HEPES PH 7.0, 15% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.498→68.648 Å / Num. all: 20273 / Num. obs: 20273 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.114 / Rsym value: 0.106 / Net I/av σ(I): 7.183 / Net I/σ(I): 18.9 / Num. measured all: 145535
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.637.20.4971.62098429150.1990.4974.399.9
2.63-2.797.20.3682.11989627480.1460.3685.8100
2.79-2.997.30.26131879525900.1040.2618100
2.99-3.237.20.1814.31770924430.0720.18111.3100
3.23-3.537.20.1171619722380.0440.1117.9100
3.53-3.957.20.07410.31484520540.030.07426100
3.95-4.567.20.04915.51303918160.0190.04936.8100
4.56-5.597.10.04317.61105415510.0170.04339.6100
5.59-7.970.04716863012350.0190.04735.4100
7.9-19.6146.40.02329.143866830.010.02361.393.6

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.35phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QMF

3qmf


Resolution: 2.5→68.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.901 / WRfactor Rfree: 0.1998 / WRfactor Rwork: 0.1478 / FOM work R set: 0.8591 / SU B: 18.321 / SU ML: 0.191 / SU R Cruickshank DPI: 0.7479 / SU Rfree: 0.2844 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.748 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1035 5.1 %RANDOM
Rwork0.1722 ---
obs0.1753 19202 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.53 Å2 / Biso mean: 31.816 Å2 / Biso min: 3.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0 Å2
2--0.86 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.5→68.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 94 232 4410
Biso mean--45.67 20.47 -
Num. residues----515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194287
X-RAY DIFFRACTIONr_bond_other_d0.0050.024049
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9725768
X-RAY DIFFRACTIONr_angle_other_deg1.13139327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9825514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76825.657198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2415728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.179159
X-RAY DIFFRACTIONr_chiral_restr0.1130.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214760
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02963
X-RAY DIFFRACTIONr_mcbond_it1.5562.1022067
X-RAY DIFFRACTIONr_mcbond_other1.5542.1012063
X-RAY DIFFRACTIONr_mcangle_it2.5963.1382566
Refine LS restraints NCS

Ens-ID: 1 / Number: 14912 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 73 -
Rwork0.21 1382 -
all-1455 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0199-0.3525-0.15121.25020.13461.0323-0.01140.06090.01720.0391-0.00160.07450.0403-0.01690.01310.0743-0.0137-0.02580.01280.0160.0287-4.338.991227.5629
21.14890.1663-0.09061.2526-0.56460.9897-0.02690.1590.1319-0.0889-0.0523-0.15560.0150.04980.07920.05320.01530.01110.09760.0690.063422.451516.705413.9802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 265
2X-RAY DIFFRACTION2B4 - 264

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