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- PDB-6ifd: Crystal Structure of CMP-N-acetylneuraminate Synthetase from Vibr... -

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Basic information

Entry
Database: PDB / ID: 6ifd
TitleCrystal Structure of CMP-N-acetylneuraminate Synthetase from Vibrio cholerae in complex with CDP and Mg2+.
ComponentsCMP-N-acetylneuraminate Synthetase
KeywordsSUGAR BINDING PROTEIN / CMP-sialic acid synthetase / bacterial / sialic acid / CTP / Mg2+
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta / CYTIDINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBose, S. / Subramanian, R.
Funding support India, 3items
OrganizationGrant numberCountry
BT/IN/SWEDEN/06/SR/2017-2018 India
BT/PR5081/INF/156/2012 India
BT/PR12422/MED/31/287/214 India
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structural and functional characterization of CMP-N-acetylneuraminate synthetase from Vibrio cholerae.
Authors: Bose, S. / Purkait, D. / Joseph, D. / Nayak, V. / Subramanian, R.
History
DepositionSep 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CMP-N-acetylneuraminate Synthetase
B: CMP-N-acetylneuraminate Synthetase
C: CMP-N-acetylneuraminate Synthetase
D: CMP-N-acetylneuraminate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,69814
Polymers113,8944
Non-polymers1,80510
Water4,378243
1
A: CMP-N-acetylneuraminate Synthetase
B: CMP-N-acetylneuraminate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0688
Polymers56,9472
Non-polymers1,1216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-25 kcal/mol
Surface area20230 Å2
MethodPISA
2
C: CMP-N-acetylneuraminate Synthetase
D: CMP-N-acetylneuraminate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6316
Polymers56,9472
Non-polymers6844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-19 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.380, 97.720, 98.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
CMP-N-acetylneuraminate Synthetase


Mass: 28473.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Production host: Escherichia coli (E. coli) / References: N-acylneuraminate cytidylyltransferase

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Non-polymers , 7 types, 253 molecules

#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 1.98 Å3/Da / Density % sol: 37.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, calcium acetate and sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→55.73 Å / Num. obs: 40516 / % possible obs: 99.4 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 1.6
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.79 / Num. unique obs: 811 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZI

1ezi


Resolution: 2.3→32.55 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.373 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.233
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2056 5.07 %RANDOM
Rwork0.202 ---
obs0.203 40516 99.3 %-
Displacement parametersBiso max: 134.51 Å2 / Biso mean: 55.93 Å2 / Biso min: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-16.0499 Å20 Å20 Å2
2---28.4042 Å20 Å2
3---12.3543 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.3→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6867 0 112 243 7222
Biso mean--68.24 55.67 -
Num. residues----896
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2364SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1187HARMONIC5
X-RAY DIFFRACTIONt_it7127HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion981SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8304SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7127HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9718HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion16.86
LS refinement shellResolution: 2.3→2.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2033 50 6.17 %
Rwork0.2375 761 -
all0.235 811 -
obs--91.45 %

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