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- PDB-5c55: Crystal structure of the Y138F mutant of C.glutamicum N-acetylneu... -

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Basic information

Entry
Database: PDB / ID: 5c55
TitleCrystal structure of the Y138F mutant of C.glutamicum N-acetylneuraminic acid lyase in complex with pyruvate
ComponentsDihydrodipicolinate synthase/N-acetylneuraminate lyase
KeywordsLYASE / Complex / Aldolase type TIM barrel / Schiff base intermediate
Function / homology
Function and homology information


N-acetylneuraminate lyase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PYRUVIC ACID / Dihydrodipicolinate synthase/N-acetylneuraminate lyase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsShen, Y. / Zhou, J. / Xie, J.
CitationJournal: To Be Published
Title: Crystal structure of the Y138F mutant of C.glutamicum N-acetylneuraminic acid lyase in complex with pyruvate
Authors: Shen, Y. / Zhou, J. / Xie, J.
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
B: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,61419
Polymers65,4862
Non-polymers1,12817
Water6,882382
1
A: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
B: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
hetero molecules

A: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
B: Dihydrodipicolinate synthase/N-acetylneuraminate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,22838
Polymers130,9724
Non-polymers2,25634
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area17620 Å2
ΔGint26 kcal/mol
Surface area39560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.893, 149.959, 143.444
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dihydrodipicolinate synthase/N-acetylneuraminate lyase


Mass: 32743.055 Da / Num. of mol.: 2 / Mutation: Y138F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / Gene: Cgl2646 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NMD2, N-acetylneuraminate lyase

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Non-polymers , 5 types, 399 molecules

#2: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris, 32% PEG 3350, 0.6 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 65906 / % possible obs: 97.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Χ2: 1.14 / Net I/av σ(I): 24.599 / Net I/σ(I): 13.6 / Num. measured all: 448127
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7370.63231620.8680.2490.6811.23895.9
1.73-1.766.90.5332100.8960.210.5721.20696.1
1.76-1.796.90.45632180.9230.1810.4921.21396.5
1.79-1.836.90.39132290.9450.1550.4221.18996.9
1.83-1.876.90.32732550.9560.130.3531.1897.3
1.87-1.916.80.28432220.9670.1130.3071.23697.2
1.91-1.966.80.25832660.9680.1040.2791.24898
1.96-2.026.90.18932520.9840.0760.2041.18697.1
2.02-2.076.80.16932790.9860.0680.1831.28198.5
2.07-2.146.80.14232770.9890.0570.1531.07798
2.14-2.226.80.11832920.9910.0470.1281.05198.3
2.22-2.316.60.11933030.9910.0490.1291.12598.4
2.31-2.416.80.09533270.9940.0380.1021.05599.2
2.41-2.546.80.0933260.9940.0370.0981.02198.7
2.54-2.76.70.08533180.9940.0350.0921.06298.6
2.7-2.916.60.07533550.9950.0320.0821.05399.3
2.91-3.26.50.06733830.9960.0280.0731.17499.4
3.2-3.666.80.05534040.9970.0220.061.02999.4
3.66-4.616.90.04234040.9980.0170.0451.12299.3
4.61-506.90.03534240.9990.0140.0381.06394.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C54

5c54


Resolution: 1.7→36.3 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.709 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1761 3345 5.1 %RANDOM
Rwork0.1443 ---
obs0.1459 62510 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.04 Å2 / Biso mean: 26.817 Å2 / Biso min: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0 Å20 Å2
2--0.89 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.7→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4543 0 72 382 4997
Biso mean--53.57 38.7 -
Num. residues----613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194700
X-RAY DIFFRACTIONr_bond_other_d0.0010.024562
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.9686374
X-RAY DIFFRACTIONr_angle_other_deg0.893310479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93224.239184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21515729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9891522
X-RAY DIFFRACTIONr_chiral_restr0.1270.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021005
LS refinement shellResolution: 1.693→1.737 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 235 -
Rwork0.205 4384 -
all-4619 -
obs--93.77 %

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