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- PDB-2i55: Complex of glucose-1,6-bisphosphate with phosphomannomutase from ... -

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Basic information

Entry
Database: PDB / ID: 2i55
TitleComplex of glucose-1,6-bisphosphate with phosphomannomutase from Leishmania mexicana
ComponentsPhosphomannomutase
KeywordsISOMERASE / HAD domain
Function / homology
Function and homology information


phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / 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
1,6-di-O-phosphono-beta-D-glucopyranose / Phosphomannomutase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSmith, B.J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of Leishmania mexicana phosphomannomutase highlights similarities with human isoforms
Authors: Kedzierski, L. / Malby, R.L. / Smith, B.J. / Perugini, M.A. / Hodder, A.N. / Ilg, T. / Colman, P.M. / Handman, E.
History
DepositionAug 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2011Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.mon_nstd_flag / _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.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_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 25, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,22012
Polymers84,3473
Non-polymers8739
Water32418
1
A: Phosphomannomutase
hetero molecules

A: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3516
Polymers56,2312
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
2
B: Phosphomannomutase
C: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0449
Polymers56,2312
Non-polymers8137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-55 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.224, 92.224, 172.824
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphomannomutase


Mass: 28115.686 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: M379 / Plasmid: pPROEX HTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q95ZD7, phosphomannomutase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-B16 / 1,6-di-O-phosphono-beta-D-glucopyranose / 1,6-di-O-phosphono-beta-D-glucose / 1,6-di-O-phosphono-D-glucose / 1,6-di-O-phosphono-glucose


Type: D-saccharide / Mass: 340.116 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Glcp1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 14% (w/v) PEG 3350, 10% PEG 400, 0.1M citrate, 50% PEG 3550, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B
DetectorDate: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17996 / % possible obs: 90.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Χ2: 1.105 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-33.40.31116451.076184.5
3-3.123.60.25817871.139192.8
3.12-3.273.50.18818051.18192.4
3.27-3.443.60.15618111.13192.2
3.44-3.653.40.1217821.094190.5
3.65-3.943.30.09517521.06189.8
3.94-4.333.50.06618051.091191.2
4.33-4.963.60.05518251.078191.6
4.96-6.243.80.05218681.141192
6.24-503.90.03819161.056189.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I54

2i54


Resolution: 2.9→46.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 36.526 / SU ML: 0.318 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 912 5.1 %RANDOM
Rwork0.192 ---
all0.195 ---
obs-17862 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.431 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å2-1.15 Å20 Å2
2---2.31 Å20 Å2
3---3.46 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 47 18 5903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226001
X-RAY DIFFRACTIONr_bond_other_d0.0010.025324
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9688087
X-RAY DIFFRACTIONr_angle_other_deg0.755312433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13824.571315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.965151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2641536
X-RAY DIFFRACTIONr_chiral_restr0.0670.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021266
X-RAY DIFFRACTIONr_nbd_refined0.2240.21431
X-RAY DIFFRACTIONr_nbd_other0.1820.25701
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22935
X-RAY DIFFRACTIONr_nbtor_other0.0870.23705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2050.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.27
X-RAY DIFFRACTIONr_mcbond_it0.4041.54608
X-RAY DIFFRACTIONr_mcbond_other0.0611.51494
X-RAY DIFFRACTIONr_mcangle_it0.50325769
X-RAY DIFFRACTIONr_scbond_it0.84332777
X-RAY DIFFRACTIONr_scangle_it1.3154.52318
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 76 -
Rwork0.271 1279 -
obs-1355 100 %
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)
110.0856-0.4352-3.26654.64465.938515.06690.307-0.2107-0.4030.87570.2932-0.44791.53020.6537-0.60020.1157-0.037-0.1125-0.0144-0.1802-0.13646.966410.641135.3052
22.38650.25570.29225.5483-3.82626.33210.53450.42360.03-0.44590.00630.10140.42211.0734-0.5408-0.09950.0850.00120.2199-0.3309-0.113123.46550.579747.7992
34.11941.6171-0.08994.4454-0.50955.92-0.09290.46610.124-0.72450.09510.229-0.1197-0.2033-0.0023-0.0993-0.03930.0176-0.1868-0.0736-0.352553.78896.2765-14.0529
47.4382-0.71640.51344.6340.40482.86370.0481-0.13211.15240.2573-0.13910.2659-0.38190.36590.091-0.2288-0.11830.0428-0.1737-0.0801-0.144440.886411.16777.0362
55.20611.24861.25876.61931.44684.7838-0.1670.45250.273-0.4168-0.15630.07880.26580.37510.3233-0.20990.0504-0.0240.00950.00320.11614.0317-5.352-13.8816
64.79460.5132-0.14955.75521.36871.89790.0423-0.27870.72490.3457-0.29611.0903-0.0495-0.16070.2538-0.2463-0.0530.069-0.2082-0.14530.008623.09452.76628.1449
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 854 - 85
21AA186 - 245186 - 245
32AA86 - 18586 - 185
43BB4 - 854 - 85
53BB186 - 245186 - 245
64BB86 - 18586 - 185
75CC4 - 854 - 85
85CC186 - 245186 - 245
96CC86 - 18586 - 185

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