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Basic information

Entry
Database: PDB / ID: 4eay
TitleCrystal structures of mannonate dehydratase from Escherichia coli strain K12 complexed with D-mannonate
ComponentsMannonate dehydratase
KeywordsLYASE / TIM Barrel / dehydratase / D-mannonate Binding
Function / homology
Function and homology information


D-glucuronate catabolic process / mannonate dehydratase / mannonate dehydratase activity / ferrous iron binding / manganese ion binding / DNA damage response
Similarity search - Function
Mannonate dehydratase / D-mannonate dehydratase (UxuA) / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-MANNONIC ACID / : / Mannonate dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsQiu, X. / Zhu, Y. / Yuan, Y. / Zhang, Y. / Liu, H. / Gao, Y. / Teng, M. / Niu, L.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural insights into decreased enzymatic activity induced by an insert sequence in mannonate dehydratase from Gram negative bacterium.
Authors: Qiu, X. / Tao, Y. / Zhu, Y. / Yuan, Y. / Zhang, Y. / Liu, H. / Gao, Y. / Teng, M. / Niu, L.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Mannonate dehydratase
B: Mannonate dehydratase
C: Mannonate dehydratase
D: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,03114
Polymers188,2774
Non-polymers75410
Water14,322795
1
A: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3564
Polymers47,0691
Non-polymers2873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3564
Polymers47,0691
Non-polymers2873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1603
Polymers47,0691
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1603
Polymers47,0691
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.470, 238.580, 54.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: -1 - 393 / Label seq-ID: 19 - 413

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Mannonate dehydratase / / D-mannonate hydrolase


Mass: 47069.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: uxuA, b4322, JW4285 / Production host: Escherichia coli (E. coli) / References: UniProt: P24215, mannonate dehydratase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CS2 / D-MANNONIC ACID / D-MANNONATE


Mass: 196.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O7
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris-HCl, 0.1M magnesium chloride hexahydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2011
RadiationMonochromator: Si(111)double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 86788 / Num. obs: 86788 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.35→2.48 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→49.55 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 14.792 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23626 4316 5 %RANDOM
Rwork0.18852 ---
obs0.19084 82253 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.413 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2---1.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12593 0 34 795 13422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212905
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.94717494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08451577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45623.832642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.193152193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.36515104
X-RAY DIFFRACTIONr_chiral_restr0.0870.21903
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219928
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_it0.4211.57876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.822212712
X-RAY DIFFRACTIONr_scbond_it1.34835029
X-RAY DIFFRACTIONr_scangle_it2.2854.54782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3128 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.320.5
Bmedium positional0.280.5
Cmedium positional0.320.5
Dmedium positional0.280.5
Amedium thermal0.582
Bmedium thermal0.472
Cmedium thermal0.52
Dmedium thermal0.462
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 303 -
Rwork0.259 6056 -
obs--99.64 %
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)
10.73710.0005-0.0721.202-0.17911.60330.0112-0.0072-0.03150.0036-0.1061-0.202-0.17050.24420.09490.0398-0.0409-0.01040.07490.03920.04340.9010.916324.7223
20.6249-0.17110.02211.8857-0.51631.351-0.0186-0.0426-0.0291-0.06410.1110.224-0.1093-0.2785-0.09240.0510.01520.00420.0880.01850.029547.406943.38025.9527
31.4497-0.2548-0.6681.0660.27061.28760.2703-0.04020.3878-0.2377-0.0358-0.3089-0.40570.1038-0.23450.2279-0.04020.11730.0273-0.00720.1693-8.04122.9197.4942
41.15150.4338-0.4161.2152-0.23880.8853-0.15150.0259-0.3266-0.17940.044-0.57130.19850.28040.10750.1530.0410.10630.1588-0.02750.33897.657368.329231.7102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 393
2X-RAY DIFFRACTION2B-1 - 393
3X-RAY DIFFRACTION3C-1 - 394
4X-RAY DIFFRACTION4D-1 - 393

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