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- PDB-3zf8: Crystal structure of Saccharomyces cerevisiae Mnn9 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3zf8
TitleCrystal structure of Saccharomyces cerevisiae Mnn9 in complex with GDP and Mn.
ComponentsMANNAN POLYMERASE COMPLEXES SUBUNIT MNN9
KeywordsTRANSFERASE
Function / homology
Function and homology information


mannan polymerase complex / mannosylation / Golgi cis cisterna / cell wall mannoprotein biosynthetic process / cis-Golgi network / protein N-linked glycosylation / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Anp1 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / Mannan polymerase complexes subunit MNN9
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.98 Å
AuthorsStriebeck, A. / Schuettelkopf, A.W. / van Aalten, D.M.F.
CitationJournal: Open Biol. / Year: 2013
Title: Yeast Mnn9 is Both a Priming Glycosyltransferase and an Allosteric Activator of Mannan Biosynthesis.
Authors: Striebeck, A. / Robinson, D.A. / Schuettelkopf, A.W. / Van Aalten, D.M.F.
History
DepositionDec 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: MANNAN POLYMERASE COMPLEXES SUBUNIT MNN9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5393
Polymers35,0411
Non-polymers4982
Water2,666148
1
A: MANNAN POLYMERASE COMPLEXES SUBUNIT MNN9
hetero molecules

A: MANNAN POLYMERASE COMPLEXES SUBUNIT MNN9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0786
Polymers70,0812
Non-polymers9964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6210 Å2
ΔGint-39.2 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.090, 57.090, 330.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2079-

HOH

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Components

#1: Protein MANNAN POLYMERASE COMPLEXES SUBUNIT MNN9 / M-POL I SUBUNIT MNN9 / M-POL II SUBUNIT MNN9


Mass: 35040.621 Da / Num. of mol.: 1 / Fragment: GLOBULAR DOMAIN, RESIDUES 93-395 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P39107
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.65 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2→55 Å / Num. obs: 23775 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.2 Å / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.98→55.15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.201 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 501 2.1 %RANDOM
Rwork0.18966 ---
obs0.19066 23134 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.075 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å20 Å2
2--1.44 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.98→55.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 29 148 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022414
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9643278
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9795286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.624.711121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62815412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.091512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211838
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.979→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 43 -
Rwork0.227 1378 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.9988 Å / Origin y: 31.6191 Å / Origin z: 11.1857 Å
111213212223313233
T0.0111 Å20.0143 Å2-0.0028 Å2-0.0431 Å2-0.0025 Å2--0.0149 Å2
L0.1153 °20.051 °2-0.0563 °2-0.1109 °20.0386 °2--0.4311 °2
S-0.0184 Å °-0.0061 Å °0.0026 Å °-0.0187 Å °0.019 Å °0.0026 Å °0.005 Å °0.016 Å °-0.0007 Å °

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