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- PDB-3o52: Structure of the E.coli GDP-mannose hydrolase (yffh) in complex w... -

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Basic information

Entry
Database: PDB / ID: 3o52
TitleStructure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate
ComponentsGDP-mannose pyrophosphatase nudK
KeywordsHYDROLASE / nudix / GDP_mannose / biofilm / tartrate / Nudix fold / GDP-mannose hydrolase
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
D(-)-TARTARIC ACID / GDP-mannose pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 27, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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
C: GDP-mannose pyrophosphatase nudK
D: GDP-mannose pyrophosphatase nudK
E: GDP-mannose pyrophosphatase nudK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,04821
Polymers108,8685
Non-polymers1,18016
Water3,549197
1
A: GDP-mannose pyrophosphatase nudK
B: GDP-mannose pyrophosphatase nudK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0668
Polymers43,5472
Non-polymers5196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-65 kcal/mol
Surface area16350 Å2
MethodPISA
2
C: GDP-mannose pyrophosphatase nudK
D: GDP-mannose pyrophosphatase nudK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0009
Polymers43,5472
Non-polymers4537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-51 kcal/mol
Surface area16660 Å2
MethodPISA
3
E: GDP-mannose pyrophosphatase nudK
hetero molecules

E: GDP-mannose pyrophosphatase nudK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9648
Polymers43,5472
Non-polymers4176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6550 Å2
ΔGint-64 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.337, 103.218, 254.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
GDP-mannose pyrophosphatase nudK


Mass: 21773.633 Da / Num. of mol.: 5
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
#2: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M KNa Tartrate, 0.1 M Bis Tris propane pH 7.5 at a ratio of 2:1 protein:reservoir, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9809 Å
DetectorType: ACSD Q210 / Detector: CCD detector / Date: Apr 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 2.5→29.73 Å / Num. obs: 33433 / % possible obs: 96.4 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.069 / Χ2: 1.121 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.544.10.34413920.74280.7
2.54-2.594.70.3314990.79488.7
2.59-2.645.70.33515810.78692.9
2.64-2.696.30.29916740.79397.9
2.69-2.757.10.27117170.78799.6
2.75-2.827.60.2217040.85399.9
2.82-2.897.90.18617450.845100
2.89-2.968.10.16516810.899100
2.96-3.058.20.13317300.922100
3.05-3.158.20.11317190.973100
3.15-3.268.20.09417221.06999.9
3.26-3.398.10.07817321.112100
3.39-3.5580.06917391.17399.8
3.55-3.735.90.06412881.31375
3.73-3.977.60.05717321.2999.6
3.97-4.277.60.05117221.38499.1
4.27-4.77.20.04517171.38698.7
4.7-5.387.50.04717571.47398.9
5.38-6.767.80.05117611.58699.4
6.76-306.50.04418211.85996.9

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Processing

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

1viu


Resolution: 2.5→29.73 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.2885 / WRfactor Rwork: 0.2112 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7733 / SU B: 24.016 / SU ML: 0.268 / SU R Cruickshank DPI: 1.0449 / SU Rfree: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 1684 5 %RANDOM
Rwork0.2112 ---
obs0.2151 33382 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.18 Å2 / Biso mean: 48.25 Å2 / Biso min: 18.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---0.43 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 70 197 7415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227311
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.989863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5775875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47324.819359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.688151368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0731546
X-RAY DIFFRACTIONr_chiral_restr0.0840.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025408
X-RAY DIFFRACTIONr_nbd_refined0.2190.23196
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24966
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2364
X-RAY DIFFRACTIONr_metal_ion_refined0.0930.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.29
X-RAY DIFFRACTIONr_mcbond_it0.5461.54372
X-RAY DIFFRACTIONr_mcangle_it1.04427087
X-RAY DIFFRACTIONr_scbond_it1.56833004
X-RAY DIFFRACTIONr_scangle_it2.6234.52775
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 115 -
Rwork0.288 1990 -
all-2105 -
obs--82.42 %
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)
13.0022-0.73720.31382.218-0.21922.16690.00780.252-0.2054-0.1964-0.0934-0.21680.14330.24920.0856-0.0407-0.0264-0.0051-0.22920.0338-0.191480.31133.35398.468
21.19820.30130.55323.44590.09951.5144-0.0127-0.03750.00070.06410.06430.3625-0.0208-0.1087-0.0516-0.12990.0208-0.0156-0.23020.0098-0.170471.18831.41107.128
33.92380.18720.68581.2760.16991.91170.08430.1061-0.34340.0740.0151-0.21920.0280.2094-0.09940.0231-0.0049-0.0262-0.2121-0.0045-0.183991.28756.28582.166
41.51010.3110.15922.5079-0.49982.5324-0.00570.33510.1348-0.0048-0.0558-0.0177-0.40410.24440.06150.0151-0.0324-0.0492-0.0481-0.0003-0.208886.85864.75972.913
54.41470.904-0.25132.353-1.35124.6288-0.18530.3138-0.3199-0.34030.30890.1440.4791-0.697-0.1236-0.0916-0.0725-0.0177-0.11160.0181-0.197351.34747.037122.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 191
2X-RAY DIFFRACTION2B4 - 191
3X-RAY DIFFRACTION3C4 - 191
4X-RAY DIFFRACTION4D4 - 191
5X-RAY DIFFRACTION5E4 - 191

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