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- PDB-6i5x: Crystal structure of Aspergillus fumigatus phosphomannomutase -

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Basic information

Entry
Database: PDB / ID: 6i5x
TitleCrystal structure of Aspergillus fumigatus phosphomannomutase
ComponentsPhosphomannomutase
KeywordsISOMERASE / Aspergillus fumigatus / phosphomannomutase
Function / homology
Function and homology information


phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / cytoplasm
Similarity search - Function
Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Eukaryotic phosphomannomutase, cap domain / Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphomannomutase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Y. / Raimi, O.G. / Ferenbach, A.T. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M004139 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of Aspergillus fumigatus phosphomannomutase
Authors: Zhang, Y. / Raimi, O.G. / Ferenbach, A.T. / van Aalten, D.M.F.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphomannomutase
B: Phosphomannomutase
C: Phosphomannomutase
D: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,21912
Polymers118,8394
Non-polymers3808
Water17,186954
1
A: Phosphomannomutase
D: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6106
Polymers59,4192
Non-polymers1904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-30 kcal/mol
Surface area23640 Å2
MethodPISA
2
B: Phosphomannomutase
C: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6106
Polymers59,4192
Non-polymers1904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-34 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.425, 102.024, 137.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phosphomannomutase


Mass: 29709.689 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Gene: CDV57_05753 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A229XZQ5, phosphomannomutase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.09 M NPS, 0.1 M MES/Imidazole pH 6.5, 20% v/v PEG500 MME, 10% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→46.6 Å / Num. obs: 56365 / % possible obs: 98 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.086 / Rrim(I) all: 0.173 / Net I/σ(I): 5.7
Reflection shellResolution: 2.2→2.279 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FUE

2fue


Resolution: 2.2→46.6 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.229 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24448 2855 5 %RANDOM
Rwork0.19824 ---
obs0.20056 54228 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.657 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.2→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8356 0 20 954 9330
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 210 -
Rwork0.222 3999 -
obs--98.62 %

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