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- PDB-5zhh: Structure of Inositol monophosphatase from Anabaena (Nostoc) sp. ... -

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Basic information

Entry
Database: PDB / ID: 5zhh
TitleStructure of Inositol monophosphatase from Anabaena (Nostoc) sp. PCC 7120
ComponentsInositol-1-monophosphatase
KeywordsHYDROLASE / Inositol monophosphatase
Function / homology
Function and homology information


: / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / metal ion binding
Similarity search - Function
Inositol monophosphatase SuhB-like / Inositol monophosphatase / 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 ...Inositol monophosphatase SuhB-like / Inositol monophosphatase / 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
Inositol-1-monophosphatase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsZhang, S.R. / Wang, F.K.
CitationJournal: To Be Published
Title: Structure of Inositol monophosphatase from Anabaena (Nostoc) sp. PCC 7120
Authors: Zhang, S.R. / Wang, F.K. / Hu, Z. / Zong, Q. / Jiang, L.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Inositol-1-monophosphatase
B: Inositol-1-monophosphatase
C: Inositol-1-monophosphatase
D: Inositol-1-monophosphatase


Theoretical massNumber of molelcules
Total (without water)116,8594
Polymers116,8594
Non-polymers00
Water14,124784
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-37 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.319, 71.568, 85.121
Angle α, β, γ (deg.)111.860, 101.420, 99.110
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...
21(CHAIN B AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...
31(CHAIN C AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...
41(CHAIN D AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: _ / Label seq-ID: 3

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(CHAIN A AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...AA
2(CHAIN B AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...BB
3(CHAIN C AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...CC
4(CHAIN D AND (RESSEQ -1:0 OR (RESID 1 AND (NAME...DD

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Components

#1: Protein
Inositol-1-monophosphatase


Mass: 29214.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all2917 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q8YT10, inositol-phosphate phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane, pH 8.8, 16% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.89→41.319 Å / Num. obs: 89610 / % possible obs: 96.1 % / Redundancy: 1.9 % / Net I/σ(I): 2.12
Reflection shellResolution: 1.89→2.52 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFL

2qfl


Resolution: 1.89→41.25 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.19 4459 4.98 %
Rwork0.17 85048 -
obs0.171 89507 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.24 Å2 / Biso mean: 36.28 Å2 / Biso min: 20.27 Å2
Refinement stepCycle: final / Resolution: 1.89→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 0 784 8304
Biso mean---45.34 -
Num. residues----985
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4157X-RAY DIFFRACTIONPOSITIONAL0
12B4157X-RAY DIFFRACTIONPOSITIONAL0
13C4157X-RAY DIFFRACTIONPOSITIONAL0
14D4157X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8924-1.91390.30281160.26652508262486
1.9139-1.93640.27451520.26052794294693
1.9364-1.96010.2651300.23742789291995
1.9601-1.98490.23661460.22272826297296
1.9849-2.0110.27751510.22692844299596
2.011-2.03850.25311430.21212807295096
2.0385-2.06770.24511560.20082811296795
2.0677-2.09850.22751630.1892846300995
2.0985-2.13130.23171530.18442816296996
2.1313-2.16630.19651540.17512878303296
2.1663-2.20360.1971300.17032814294496
2.2036-2.24370.22381450.18112868301396
2.2437-2.28680.21621550.19032730288595
2.2868-2.33350.19711520.17612890304297
2.3335-2.38420.22011620.1752807296996
2.3842-2.43970.17851540.16572876303097
2.4397-2.50070.241530.18012789294296
2.5007-2.56830.19491360.16922896303296
2.5683-2.64390.19811570.17552870302796
2.6439-2.72920.18221440.17122777292196
2.7292-2.82670.18351670.17282872303997
2.8267-2.93980.21551460.17462902304898
2.9398-3.07360.19391450.17692863300897
3.0736-3.23560.18291460.17512891303798
3.2356-3.43820.1931400.17692891303197
3.4382-3.70350.16911610.16972872303397
3.7035-4.07590.16241640.15262830299497
4.0759-4.6650.17421440.13222933307798
4.665-5.87470.16071260.14572885301198
5.8747-41.26420.16351680.16882873304198
Refinement TLS params.Method: refined / Origin x: -25.6138 Å / Origin y: -17.0856 Å / Origin z: 27.8413 Å
111213212223313233
T0.1981 Å20.0148 Å2-0.0061 Å2-0.2083 Å20.0118 Å2--0.2357 Å2
L0.2506 °20.0401 °20.0063 °2-0.2696 °20.3792 °2--0.944 °2
S0.0508 Å °0.0018 Å °-0.0059 Å °0.0062 Å °-0.0085 Å °-0.0203 Å °0.001 Å °-0.0483 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA-1 - 266
2X-RAY DIFFRACTION1ALLA301 - 512
3X-RAY DIFFRACTION1ALLB-1 - 266
4X-RAY DIFFRACTION1ALLB301 - 494
5X-RAY DIFFRACTION1ALLC-2 - 266
6X-RAY DIFFRACTION1ALLC301 - 497
7X-RAY DIFFRACTION1ALLD-2 - 267
8X-RAY DIFFRACTION1ALLD301 - 481

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