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- PDB-7zvm: Thermococcus barophilus phosphomannose isomerase protein structur... -

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Basic information

Entry
Database: PDB / ID: 7zvm
TitleThermococcus barophilus phosphomannose isomerase protein structure at 1.6 A
ComponentsMannose-6-phosphate isomerase
KeywordsISOMERASE / High pressure / protein dynamics / Neutron scaterring
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / isomerase activity / RmlC-like jelly roll fold / Mannose-6-phosphate isomerase
Function and homology information
Biological speciesThermococcus barophilus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsHoh, F. / Calio, A.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Int J Mol Sci / Year: 2022
Title: Unravelling the Adaptation Mechanisms to High Pressure in Proteins.
Authors: Calio, A. / Dubois, C. / Fontanay, S. / Koza, M.M. / Hoh, F. / Roumestand, C. / Oger, P. / Peters, J.
History
DepositionMay 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4102
Polymers13,3851
Non-polymers241
Water1,08160
1
A: Mannose-6-phosphate isomerase
hetero molecules

A: Mannose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8194
Polymers26,7712
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1920 Å2
ΔGint-42 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.482, 52.410, 112.868
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-358-

HOH

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Components

#1: Protein Mannose-6-phosphate isomerase


Mass: 13385.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First and last aa are not visible / Source: (gene. exp.) Thermococcus barophilus (archaea) / Strain: DSM 11836 / MP / Gene: TERMP_00744 / Production host: Escherichia coli (E. coli) / References: UniProt: F0LL70
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.12 M monosaccharide mix, 0.1M buffer system 2 pH 8.5 and 50% V/V MPD (F7 Morpheus conditions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.58→47.58 Å / Num. obs: 38008 / % possible obs: 98.9 % / Redundancy: 3.39 % / CC1/2: 0.997 / Net I/σ(I): 7.66
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 1050 / CC1/2: 0.18

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold2

Resolution: 1.58→47.58 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.1635 / FOM work R set: 0.7698 / SU B: 5.024 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0818 / SU Rfree: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1011 5 %RANDOM
Rwork0.1735 ---
obs0.1754 19202 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.48 Å2 / Biso mean: 27.176 Å2 / Biso min: 15.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20 Å2
2--0.01 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 1.58→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 1 60 932
Biso mean--47.25 42.18 -
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.013897
X-RAY DIFFRACTIONr_bond_other_d0.0010.016856
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.6551212
X-RAY DIFFRACTIONr_angle_other_deg1.4071.5861984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97922.91748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40215161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.918154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02204
X-RAY DIFFRACTIONr_rigid_bond_restr4.38831753
LS refinement shellResolution: 1.58→1.617 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.516 71 -
Rwork-1354 -
obs--95.57 %

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