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- PDB-7zvy: Thermococcus kadokarensis phosphomannose isomerase -

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Basic information

Entry
Database: PDB / ID: 7zvy
TitleThermococcus kadokarensis phosphomannose isomerase
Components(Cupin_2 domain-containing ...) x 4
KeywordsISOMERASE / High pressure adaptation / proteins dynamics / neutron scattering
Function / homology
Function and homology information


: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupin type-2 domain-containing protein
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 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 17, 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

Downloads & links

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Assembly

Deposited unit
A: Cupin_2 domain-containing protein
B: Cupin_2 domain-containing protein
C: Cupin_2 domain-containing protein
D: Cupin_2 domain-containing protein
E: Cupin_2 domain-containing protein
F: Cupin_2 domain-containing protein
G: Cupin_2 domain-containing protein
H: Cupin_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,90812
Polymers105,6468
Non-polymers2624
Water90150
1
A: Cupin_2 domain-containing protein
G: Cupin_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0385
Polymers25,8412
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-118 kcal/mol
Surface area10290 Å2
2
B: Cupin_2 domain-containing protein
E: Cupin_2 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,1942
Polymers26,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-21 kcal/mol
Surface area10440 Å2
3
C: Cupin_2 domain-containing protein
D: Cupin_2 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,1572
Polymers27,1572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-26 kcal/mol
Surface area10660 Å2
4
F: Cupin_2 domain-containing protein
H: Cupin_2 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5203
Polymers26,4542
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-47 kcal/mol
Surface area10350 Å2
Unit cell
Length a, b, c (Å)91.158, 91.158, 113.378
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Cupin 2 domain-containing ... , 4 types, 8 molecules ACDFBEHG

#1: Protein
Cupin_2 domain-containing protein


Mass: 13578.505 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0503 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD98
#2: Protein Cupin_2 domain-containing protein


Mass: 13318.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Missing Nt 1-2 and Ct 113-116 / Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0503 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD98
#3: Protein Cupin_2 domain-containing protein


Mass: 12875.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0503 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD98
#4: Protein Cupin_2 domain-containing protein


Mass: 12262.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0503 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD98

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Non-polymers , 2 types, 54 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2M ammonium phosphate, 0.1M Tris pH 8.5 and 50 % V/V MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.288
11K, H, -L20.235
11-h,-k,l30.243
11-K, -H, -L40.233
ReflectionResolution: 2.16→64.79 Å / Num. obs: 53371 / % possible obs: 99.2 % / Redundancy: 2.2 % / CC1/2: 0.997 / Net I/σ(I): 7.8
Reflection shellResolution: 2.16→2.2 Å / Rmerge(I) obs: 0.661 / Num. unique obs: 5036 / CC1/2: 0.297 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold2

Resolution: 2.16→64.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.897 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 1994 3.6 %RANDOM
Rwork0.2208 ---
obs0.2233 53371 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.33 Å2 / Biso mean: 63.241 Å2 / Biso min: 29.66 Å2
Baniso -1Baniso -2Baniso -3
1--14.11 Å2-0 Å2-0 Å2
2---14.11 Å2-0 Å2
3---28.22 Å2
Refinement stepCycle: final / Resolution: 2.16→64.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 4 50 7172
Biso mean--50 55.48 -
Num. residues----856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0137392
X-RAY DIFFRACTIONr_bond_other_d0.0070.0167005
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.64910004
X-RAY DIFFRACTIONr_angle_other_deg1.4341.58616181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9995867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23722.618401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.697151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1541538
X-RAY DIFFRACTIONr_chiral_restr0.0890.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028217
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021699
X-RAY DIFFRACTIONr_rigid_bond_restr9.629314397
LS refinement shellResolution: 2.161→2.217 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.314 134 -
Rwork-3733 -
obs--93 %

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