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- PDB-6cfr: Structure of Human alpha-Phosphomannomutase 1 containing mutation... -

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Basic information

Entry
Database: PDB / ID: 6cfr
TitleStructure of Human alpha-Phosphomannomutase 1 containing mutation R183I
ComponentsPhosphomannomutase 1
KeywordsISOMERASE / phosphatase / haloalkanoate dehalogenase superfamily / mutase
Function / homology
Function and homology information


Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / cellular response to leukemia inhibitory factor / neuronal cell body / metal ion binding / cytosol
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
Phosphomannomutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsJi, T. / Dunaway-Mariano, D. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103403 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis of the Molecular Switch between Phosphatase and Mutase Functions of Human Phosphomannomutase 1 under Ischemic Conditions.
Authors: Ji, T. / Zhang, C. / Zheng, L. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionFeb 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7913
Polymers29,7431
Non-polymers492
Water6,053336
1
A: Phosphomannomutase 1
hetero molecules

A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5836
Polymers59,4862
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2650 Å2
ΔGint-34 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.910, 51.910, 216.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

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Components

#1: Protein Phosphomannomutase 1 / PMM 1 / PMMH-22


Mass: 29742.775 Da / Num. of mol.: 1 / Mutation: R183I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PMM1, PMMH22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92871, phosphomannomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350, 0.15 M DL-malate, pH 7.0, 50 mM MgCl2, and 8 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.07→42.11 Å / Num. obs: 18258 / % possible obs: 96.04 % / Redundancy: 2 % / Net I/σ(I): 9.08
Reflection shellResolution: 2.07→2.126 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FUC

2fuc


Resolution: 2.07→42.11 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.02
RfactorNum. reflection% reflection
Rfree0.2121 1838 10.07 %
Rwork0.1692 --
obs0.1736 18256 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.07→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 2 336 2301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072006
X-RAY DIFFRACTIONf_angle_d1.012700
X-RAY DIFFRACTIONf_dihedral_angle_d13.271758
X-RAY DIFFRACTIONf_chiral_restr0.076290
X-RAY DIFFRACTIONf_plane_restr0.005357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.1260.27811250.20041121X-RAY DIFFRACTION89
2.126-2.18850.27041420.19341254X-RAY DIFFRACTION97
2.1885-2.25920.27521350.17451235X-RAY DIFFRACTION97
2.2592-2.33990.26041350.17481247X-RAY DIFFRACTION97
2.3399-2.43360.21061390.17241238X-RAY DIFFRACTION97
2.4336-2.54430.2031410.17431239X-RAY DIFFRACTION97
2.5443-2.67840.23821420.17871266X-RAY DIFFRACTION97
2.6784-2.84620.24721410.18231270X-RAY DIFFRACTION97
2.8462-3.06590.22261450.18211289X-RAY DIFFRACTION97
3.0659-3.37430.18971410.16491260X-RAY DIFFRACTION97
3.3743-3.86230.17721450.15211298X-RAY DIFFRACTION97
3.8623-4.8650.16781490.14311309X-RAY DIFFRACTION96
4.865-42.12140.21131580.17671392X-RAY DIFFRACTION94

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