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- PDB-4n81: Another flexible region at the active site of an inositol monopho... -

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Basic information

Entry
Database: PDB / ID: 4n81
TitleAnother flexible region at the active site of an inositol monophosphatase from Zymomonas mobilis
ComponentsInositol monophosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


phosphoric ester hydrolase activity / L-histidine biosynthetic process / 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
Inositol monophosphatase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsHwang, H.J. / Park, S.Y. / Kim, J.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of cbbF from Zymomonas mobilis and its functional implication
Authors: Hwang, H.J. / Park, S.Y. / Kim, J.S.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7752
Polymers28,6791
Non-polymers961
Water5,260292
1
A: Inositol monophosphatase
hetero molecules

A: Inositol monophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5494
Polymers57,3572
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3530 Å2
ΔGint-32 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.747, 90.747, 75.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Inositol monophosphatase / IMPase/FBPase


Mass: 28678.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Strain: ZM4 / Gene: ZMO1518 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NMB8, inositol-phosphate phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 11%(w/v) polyethylene glycol 4000, 0.2M Lithium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 28603 / Num. obs: 28603 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.22 Å2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→39.295 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9026 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 16.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 2832 9.91 %RANDOM
Rwork0.1458 ---
all0.1491 28577 --
obs0.1491 28577 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.7 Å2 / Biso mean: 24.4505 Å2 / Biso min: 7.48 Å2
Refinement stepCycle: LAST / Resolution: 1.901→39.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 5 292 2270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192032
X-RAY DIFFRACTIONf_angle_d1.7212757
X-RAY DIFFRACTIONf_chiral_restr0.15302
X-RAY DIFFRACTIONf_plane_restr0.011365
X-RAY DIFFRACTIONf_dihedral_angle_d13.866751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9009-1.93370.22791550.164212821437
1.9337-1.96880.21731300.15512691399
1.9688-2.00670.1921330.153412691402
2.0067-2.04760.19051330.146712881421
2.0476-2.09220.20281300.13812731403
2.0922-2.14080.17681280.142112991427
2.1408-2.19440.15871290.132512571386
2.1944-2.25370.17451500.138712691419
2.2537-2.320.19011570.142912571414
2.32-2.39490.19791340.146712911425
2.3949-2.48040.19391470.136812521399
2.4804-2.57970.17481360.146913031439
2.5797-2.69710.17211590.146812631422
2.6971-2.83930.17251640.152612631427
2.8393-3.01710.19331540.150812821436
3.0171-3.250.17191390.154412881427
3.25-3.57680.17471370.143813131450
3.5768-4.09390.16911210.132613171438
4.0939-5.15610.15561370.13113381475
5.1561-39.3030.18261590.173413721531
Refinement TLS params.Method: refined / Origin x: 10.474 Å / Origin y: 39.9509 Å / Origin z: 27.5964 Å
111213212223313233
T0.1095 Å20.0004 Å2-0.024 Å2-0.1557 Å20.0064 Å2--0.1016 Å2
L1.3151 °2-0.6558 °2-0.3685 °2-1.658 °20.0822 °2--0.7318 °2
S0.0743 Å °0.2606 Å °-0.0522 Å °-0.2046 Å °-0.0643 Å °0.1116 Å °-0.0012 Å °-0.0962 Å °-0.0237 Å °
Refinement TLS groupSelection details: ALL

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