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- PDB-2i54: Phosphomannomutase from Leishmania mexicana -

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Basic information

Entry
Database: PDB / ID: 2i54
TitlePhosphomannomutase 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
CITRIC ACID / Phosphomannomutase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.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.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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,06711
Polymers84,3473
Non-polymers7208
Water5,044280
1
A: Phosphomannomutase
hetero molecules

A: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7358
Polymers56,2312
Non-polymers5046
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)56,7007
Polymers56,2312
Non-polymers4685
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-28 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.413, 92.413, 173.249
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1001-

CL

DetailsThe biological assembly is a dimer formed by chains B and C, or by a two-fold rotation of chain A.

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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) / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 14% (w/v) PEG3350, 10% PEG 400, 0.1M citrate, 50% PEG3550, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.979417, 0.979564, 0.984011
DetectorDate: Apr 6, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794171
20.9795641
30.9840111
ReflectionResolution: 2.1→30 Å / Num. all: 50650 / Num. obs: 50609 / % possible obs: 99.8 %
Reflection shellHighest resolution: 2.1 Å / Rmerge(I) obs: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.029 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2572 5.1 %RANDOM
Rwork0.189 ---
all0.191 ---
obs-50609 99.79 %-
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: 45.548 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å20 Å2
2---0.37 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 44 280 6162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226034
X-RAY DIFFRACTIONr_bond_other_d0.0010.025354
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9618129
X-RAY DIFFRACTIONr_angle_other_deg0.86312502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20124.571315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.915151069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8471536
X-RAY DIFFRACTIONr_chiral_restr0.0930.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021266
X-RAY DIFFRACTIONr_nbd_refined0.2060.21256
X-RAY DIFFRACTIONr_nbd_other0.1860.25457
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22929
X-RAY DIFFRACTIONr_nbtor_other0.0870.23448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.219
X-RAY DIFFRACTIONr_mcbond_it0.8011.54634
X-RAY DIFFRACTIONr_mcbond_other0.1641.51494
X-RAY DIFFRACTIONr_mcangle_it0.97225783
X-RAY DIFFRACTIONr_scbond_it1.74932826
X-RAY DIFFRACTIONr_scangle_it2.4954.52346
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 182 -
Rwork0.239 3494 -
obs-3676 99.97 %
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)
16.7122-0.0787-2.14273.74283.24098.94450.0252-0.2335-0.14970.38110.3886-0.37230.79660.6092-0.41370.0034-0.0384-0.0171-0.0337-0.1701-0.13446.859911.291434.8061
22.2361-0.06280.66274.6346-1.79053.27290.31250.4006-0.0954-0.5082-0.0280.11280.22630.4129-0.2845-0.07640.0483-0.0096-0.0229-0.1686-0.176423.13420.40847.9022
33.83731.1157-0.71452.95180.44894.8949-0.00530.54740.1112-0.44820.09320.0527-0.1385-0.2638-0.088-0.16310.00210.022-0.1759-0.0279-0.291854.38566.5768-14.1106
45.89640.09570.6372.0275-0.11343.24290.1233-0.08080.99310.2665-0.12830.2527-0.52370.23040.0049-0.0947-0.08440.1039-0.2299-0.0678-0.076440.734311.76416.4834
57.19172.41962.37474.95222.23834.952-0.38780.78330.8061-0.16540.03230.49640.18120.41010.3555-0.21670.03310.03090.04170.14440.065314.2278-5.2413-15.0106
63.10681.5567-0.45695.60310.12172.18520.263-0.14520.76960.5354-0.30811.2266-0.1924-0.34440.0451-0.1368-0.0280.2012-0.1801-0.13550.113322.93543.19797.1998
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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