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- PDB-1zx5: The structure of a putative mannosephosphate isomerase from Archa... -

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Basic information

Entry
Database: PDB / ID: 1zx5
TitleThe structure of a putative mannosephosphate isomerase from Archaeoglobus fulgidus
Componentsmannosephosphate isomerase, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / mannose 6-phosphate / isomerase / Archaeoglobus fulgidus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


mannose-6-phosphate isomerase / mannose-6-phosphate isomerase activity / carbohydrate metabolic process / zinc ion binding
Similarity search - Function
Mannose-6-phosphate isomerase, Firmicutes type, short form / : / : / Mannose-6-phosphate isomerase, cupin domain / Mannose-6-phosphate isomerase, type I / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I C-terminal / Phosphomannose isomerase type I, catalytic domain / RmlC-like cupin domain superfamily / Jelly Rolls ...Mannose-6-phosphate isomerase, Firmicutes type, short form / : / : / Mannose-6-phosphate isomerase, cupin domain / Mannose-6-phosphate isomerase, type I / Phosphomannose isomerase type I, catalytic domain / Phosphomannose isomerase type I C-terminal / Phosphomannose isomerase type I, catalytic domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / beta-L-fructofuranose / mannose-6-phosphate isomerase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsCuff, M.E. / Skarina, T. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a putative mannosephosphate isomerase from Archaeoglobus fulgidus
Authors: Cuff, M.E. / Skarina, T. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionJun 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mannosephosphate isomerase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,54011
Polymers33,7841
Non-polymers75710
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.045, 160.045, 160.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-941-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein mannosephosphate isomerase, putative


Mass: 33783.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0035 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / References: UniProt: O30200
#2: Sugar ChemComp-LFR / beta-L-fructofuranose


Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LFrufbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fructofuranoseCOMMON NAMEGMML 1.0
b-L-FrufIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 255 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 4.5 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: PEG 5k MME, Na Acetate, ethylene glycol, sucrose, glycerol, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→37.72 Å / Num. all: 31599 / Num. obs: 31599 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 45.8 Å2 / Rsym value: 0.072 / Net I/σ(I): 9.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.446 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.3→37.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.375 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.134
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19081 1593 5 %RANDOM
Rwork0.16243 ---
all0.16383 31599 --
obs0.16383 30005 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.343 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 50 246 2666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222511
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.9723383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17924.569116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46915444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5611513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021900
X-RAY DIFFRACTIONr_nbd_refined0.1890.21031
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21676
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.220
X-RAY DIFFRACTIONr_mcbond_it0.8641.51578
X-RAY DIFFRACTIONr_mcangle_it1.22722445
X-RAY DIFFRACTIONr_scbond_it1.95131059
X-RAY DIFFRACTIONr_scangle_it3.1474.5937
LS refinement shellResolution: 2.302→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 120 -
Rwork0.201 2162 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: 76.5518 Å / Origin y: 96.9253 Å / Origin z: 39.5673 Å
111213212223313233
T-0.0559 Å2-0.0391 Å2-0.0065 Å2--0.1164 Å20.0286 Å2---0.0569 Å2
L0.9765 °20.0117 °2-0.0041 °2-1.3837 °2-0.9083 °2--1.5815 °2
S-0.0511 Å °-0.0048 Å °-0.0008 Å °0.0698 Å °-0.0358 Å °-0.1535 Å °0.0062 Å °0.0595 Å °0.0869 Å °

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