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- PDB-5ue7: Crystal structure of the phosphomannomutase PMM1 from Candida alb... -

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Basic information

Entry
Database: PDB / ID: 5ue7
TitleCrystal structure of the phosphomannomutase PMM1 from Candida albicans, apoenzyme state
ComponentsPhosphomannomutase
KeywordsISOMERASE / phosphomannomutase / mannose-6-phosphate / mannose-1-phosphate / HAD domain / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / National Institute of Allergy and Infectious Diseases / NIAID
Function / homology
Function and homology information


phosphomannomutase / phosphomannomutase activity / fungal biofilm matrix / GDP-mannose biosynthetic process / mannose metabolic process / protein targeting to ER / protein N-linked glycosylation / 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
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of the phosphomannomutase PMM1 from Candida albicans, apoenzyme state
Authors: Stogios, P.J.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.title / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphomannomutase
B: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2447
Polymers58,1112
Non-polymers1335
Water11,187621
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-41 kcal/mol
Surface area24690 Å2
2
A: Phosphomannomutase
hetero molecules

B: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2447
Polymers58,1112
Non-polymers1335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y+1/2,-z+5/21
Buried area2610 Å2
ΔGint-50 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.225, 80.719, 116.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-649-

HOH

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Components

#1: Protein Phosphomannomutase / / PMM


Mass: 29055.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: PMM1, CaO19.10454, CaO19.2937 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P31353, 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3350, 0.2 M MgCl2, 0.1 M Bis-tris pH 5.5, 1% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 19, 2016
RadiationMonochromator: 1.5418 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 43607 / % possible obs: 99.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 36.97
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.75 / Num. unique all: 2119 / CC1/2: 0.675 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AMY

2amy


Resolution: 1.95→24.696 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 1996 4.59 %RANDOM
Rwork0.2083 ---
obs0.2104 43507 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→24.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 5 621 4710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054182
X-RAY DIFFRACTIONf_angle_d0.7225644
X-RAY DIFFRACTIONf_dihedral_angle_d16.2551564
X-RAY DIFFRACTIONf_chiral_restr0.048599
X-RAY DIFFRACTIONf_plane_restr0.005742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9446-1.99320.29861340.27812768X-RAY DIFFRACTION95
1.9932-2.0470.33511390.27842915X-RAY DIFFRACTION99
2.047-2.10730.30791400.25982902X-RAY DIFFRACTION99
2.1073-2.17520.28261420.26412934X-RAY DIFFRACTION99
2.1752-2.25290.35411400.31482921X-RAY DIFFRACTION98
2.2529-2.34310.30761410.27432905X-RAY DIFFRACTION98
2.3431-2.44960.27251430.23462971X-RAY DIFFRACTION100
2.4496-2.57860.27041420.22682963X-RAY DIFFRACTION100
2.5786-2.740.27291430.21582969X-RAY DIFFRACTION100
2.74-2.95120.24711440.22232982X-RAY DIFFRACTION100
2.9512-3.24760.28831430.2123008X-RAY DIFFRACTION100
3.2476-3.71620.21541450.19323016X-RAY DIFFRACTION100
3.7162-4.67680.24121470.16213059X-RAY DIFFRACTION100
4.6768-24.69840.21741530.17543198X-RAY DIFFRACTION100
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)
15.56411.7164-1.95450.9010.32425.0805-0.32172.2932-0.0842-0.33650.21790.24830.0907-1.5450.12510.3554-0.05590.02291.0972-0.10460.38793.1809100.3564115.8084
22.11-0.1311-0.19752.96360.09830.6131-0.07070.1353-0.1505-0.02780.03220.0031-0.0269-0.08330.03790.2704-0.01630.04040.175-0.00870.2136-4.1544112.24144.8964
31.4252-0.7181-0.2361.76530.39471.26670.0472-0.010.09960.17120.027-0.2428-0.12390.1529-0.05330.3022-0.03170.0440.2053-0.01350.26165.8243115.4217144.8993
40.8085-1.2254-0.71093.2926-0.51222.527-0.9841.1207-1.6577-0.1111-0.443-0.22581.7571-0.2016-0.50210.6518-0.07850.40950.292-0.27170.73419.344490.767124.6158
55.51740.0365-3.81892.5048-0.08245.45810.18260.40340.2442-0.0643-0.0589-0.0801-0.48250.1179-0.07010.2625-0.00970.0020.36560.01710.293816.0228104.2047119.0235
62.7044-1.04260.07411.79460.15163.7767-0.5229-1.81541.72650.4935-0.06110.6779-1.0694-0.87730.50.55010.1551-0.1650.868-0.35240.931626.6417111.0877172.002
73.16810.71882.78291.34430.24173.9770.2057-3.17180.01230.0398-0.28180.26130.4605-2.09460.03370.2549-0.01790.03691.4288-0.06020.504619.60798.4978171.7628
81.3349-0.0068-0.31243.37090.23951.6357-0.0686-0.1437-0.0777-0.0570.003-0.38180.10440.25380.07190.25540.02320.04310.23120.02360.259417.701680.6567145.8177
97.11971.10043.71271.4750.78315.575-0.0038-0.44930.0196-0.0039-0.1285-0.21650.12580.12250.11470.1761-0.00040.02450.26410.00660.293330.946199.1566164.6674
104.14950.5348-0.48489.09132.25849.7761-0.1517-0.56740.22181.8164-0.64020.35930.3441-0.06280.59380.58080.08150.00050.8184-0.1360.43134.7526105.2185181.2222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:85)
2X-RAY DIFFRACTION2(chain A and resid 86:140)
3X-RAY DIFFRACTION3(chain A and resid 141:193)
4X-RAY DIFFRACTION4(chain A and resid 194:209)
5X-RAY DIFFRACTION5(chain A and resid 210:252)
6X-RAY DIFFRACTION6(chain B and resid 2:15)
7X-RAY DIFFRACTION7(chain B and resid 16:86)
8X-RAY DIFFRACTION8(chain B and resid 87:189)
9X-RAY DIFFRACTION9(chain B and resid 190:247)
10X-RAY DIFFRACTION10(chain B and resid 248:252)

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