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- PDB-2fue: Human alpha-Phosphomannomutase 1 with D-mannose 1-phosphate and M... -

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Basic information

Entry
Database: PDB / ID: 2fue
TitleHuman alpha-Phosphomannomutase 1 with D-mannose 1-phosphate and Mg2+ cofactor bound
ComponentsPhosphomannomutase 1
KeywordsISOMERASE / Phosphomannomutase / enzyme-product complex / protein glycosylation / carbohydrate-deficient glycoprotein syndrome / Haloalkanoic Acid Dehalogenase Superfamily
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
1-O-phosphono-alpha-D-mannopyranose / Phosphomannomutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsSilvaggi, N.R. / Zhang, C. / Lu, Z. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The X-ray crystal structures of human alpha-phosphomannomutase 1 reveal the structural basis of congenital disorder of glycosylation type 1a.
Authors: Silvaggi, N.R. / Zhang, C. / Lu, Z. / Dai, J. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)30,2834
Polymers29,9741
Non-polymers3093
Water4,288238
1
A: Phosphomannomutase 1
hetero molecules

A: Phosphomannomutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5668
Polymers59,9492
Non-polymers6176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)51.390, 51.390, 214.603
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-1007-

HOH

DetailsThe asymmetric unit contains one monomer of the biologically active dimer. The dimer can be generated by applying the following matrix to the deposited coordinates: | 3.123e-17, 1, 5.881e-16| | 1,-1.745e-16, 1.109e-15| | 1.049e-15, 5.487e-16, -1| (-7.416e-14,-1.349e-13, 216)

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Components

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


Mass: 29974.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q92871, phosphomannomutase
#2: Sugar ChemComp-M1P / 1-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE 1-PHOSPHATE / 1-O-phosphono-alpha-D-mannose / 1-O-phosphono-D-mannose / 1-O-phosphono-mannose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Manp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growDetails: Crystals grown by hanging drop vapor diffusion over mother liquor containing 15-18% polyethylene glycol 3350, 0.15M D,L-malic acid, pH 7.0, 50mM MgCL2, and 8mM 2-mercaptoethanol. Drops were ...Details: Crystals grown by hanging drop vapor diffusion over mother liquor containing 15-18% polyethylene glycol 3350, 0.15M D,L-malic acid, pH 7.0, 50mM MgCL2, and 8mM 2-mercaptoethanol. Drops were formed by mixing 2ul of protein solution (10mM HEPES, pH 7.5, 100mM NaCl, 5mM MgCl2) at 15-25mg/ml with 2ul of mother liquor. Crystals grew after one to three days at 296 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 28735 / Num. obs: 28735 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 42.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4 / % possible all: 75.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT1.701data extraction
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2FUC

2fuc


Resolution: 1.75→24.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.585 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24033 1464 5.1 %RANDOM
Rwork0.20238 ---
obs0.20422 27230 95 %-
all-28694 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.633 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2--1.13 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 18 238 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222011
X-RAY DIFFRACTIONr_bond_other_d0.0040.021435
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9752712
X-RAY DIFFRACTIONr_angle_other_deg0.81333456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5723.40297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54415351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7961517
X-RAY DIFFRACTIONr_chiral_restr0.0670.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_nbd_refined0.2090.2410
X-RAY DIFFRACTIONr_nbd_other0.1960.21504
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21010
X-RAY DIFFRACTIONr_nbtor_other0.0840.21026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3210.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6481.51519
X-RAY DIFFRACTIONr_mcbond_other0.121.5506
X-RAY DIFFRACTIONr_mcangle_it0.73121972
X-RAY DIFFRACTIONr_scbond_it1.3383860
X-RAY DIFFRACTIONr_scangle_it1.8494.5739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 87 -
Rwork0.236 1478 -
obs--72.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.62130.0055-0.93852.40530.73342.7664-0.10210.063-0.05820.0363-0.00460.19640.151-0.18510.1067-0.09890.00570.0648-0.1265-0.0028-0.068823.93538.141284.1124
21.7482-0.1315-0.46631.95210.0142.42890.01420.1477-0.0242-0.17470.05540.0741-0.10510.0197-0.0697-0.079400.0254-0.0989-0.0071-0.134732.162931.952497.673
30.6530.14760.98583.35751.38841.8970.0398-0.0493-0.12340.33610.2571-0.25260.32850.0684-0.29690.03270.0470.0324-0.0171-0.0348-0.017337.048115.031296.8167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 9013 - 90
2X-RAY DIFFRACTION1AA198 - 257198 - 257
3X-RAY DIFFRACTION2AA98 - 19098 - 190
4X-RAY DIFFRACTION3AA91 - 9791 - 97
5X-RAY DIFFRACTION3AA191 - 197191 - 197

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