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- PDB-3o69: Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in com... -

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Basic information

Entry
Database: PDB / ID: 3o69
TitleStructure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with Mg++
ComponentsGDP-mannose pyrophosphatase nudK
KeywordsHYDROLASE / nudix / GDP_mannose / biofilm
Function / homology
Function and homology information


GDP-mannose hydrolase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Nucleoside diphosphate pyrophosphatase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / GDP-mannose pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAmzel, L.M. / Gabelli, S.B. / Boto, A.N.
CitationJournal: Proteins / Year: 2011
Title: Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition.
Authors: Boto, A.N. / Xu, W. / Jakoncic, J. / Pannuri, A. / Romeo, T. / Bessman, M.J. / Gabelli, S.B. / Amzel, L.M.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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.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_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_ref_seq_dif.details / _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: GDP-mannose pyrophosphatase nudK
B: GDP-mannose pyrophosphatase nudK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,91614
Polymers43,4312
Non-polymers48512
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-103 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.379, 69.260, 98.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GDP-mannose pyrophosphatase nudK


Mass: 21715.598 Da / Num. of mol.: 2 / Mutation: E100A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2467, JW2451, nudK, yffH / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P37128, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 387 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 48.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20-26% PEG 3350, 0.2 M Mg Cl, 0.1 M Tris HCL pH 8.5, 4mM GDP-mannose at a ratio of 1:1 protein:reservoir, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→22.81 Å / Num. obs: 23871 / % possible obs: 96 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.089 / Χ2: 2.653 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.183.30.33118272.37875.1
2.18-2.263.80.25721722.78489.3
2.26-2.375.10.30424292.45998.4
2.37-2.496.60.22224272.45299.9
2.49-2.656.50.18624712.57799.9
2.65-2.856.40.15224482.702100
2.85-3.146.20.10924742.71699.6
3.14-3.596.10.07624792.86999.6
3.59-4.525.70.05725133.01899.4
4.52-505.80.04926312.45998.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O52

3o52


Resolution: 2.1→22.81 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.868 / WRfactor Rfree: 0.2494 / WRfactor Rwork: 0.1855 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7928 / SU B: 5.468 / SU ML: 0.148 / SU R Cruickshank DPI: 0.2677 / SU Rfree: 0.2333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 1200 5.1 %RANDOM
Rwork0.2048 ---
obs0.2084 23750 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.46 Å2 / Biso mean: 24.7644 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→22.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 24 375 3331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222997
X-RAY DIFFRACTIONr_bond_other_d0.0070.0210
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9734038
X-RAY DIFFRACTIONr_angle_other_deg1.16322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61324.73148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29215558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3781520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022216
X-RAY DIFFRACTIONr_nbd_refined0.2030.21386
X-RAY DIFFRACTIONr_nbd_other0.4360.219
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21990
X-RAY DIFFRACTIONr_nbtor_other0.070.23
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2343
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.231
X-RAY DIFFRACTIONr_mcbond_it0.6551.51807
X-RAY DIFFRACTIONr_mcangle_it1.22622924
X-RAY DIFFRACTIONr_scbond_it1.79731216
X-RAY DIFFRACTIONr_scangle_it2.9244.51114
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 56 -
Rwork0.221 1261 -
all-1317 -
obs--73.09 %

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