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- PDB-1ybd: Crystal structure analysis of uridylate kinase from Neisseria men... -

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Basic information

Entry
Database: PDB / ID: 1ybd
TitleCrystal structure analysis of uridylate kinase from Neisseria meningitidis
ComponentsUridylate kinase
KeywordsTRANSFERASE / alpha/beta/alpha fold / Kinase / Hexamer / Structural Genomics / Protein Structure Initiative / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC / T1843
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Uridylate kinase, bacteria / Uridylate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Uridylate kinase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsKumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure analysis of uridylate kinase from Neisseria meningitidis
Authors: Kumaran, D. / Swaminathan, S.
History
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Uridylate kinase
B: Uridylate kinase
C: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1947
Polymers78,8713
Non-polymers3224
Water2,018112
1
A: Uridylate kinase
C: Uridylate kinase
hetero molecules

A: Uridylate kinase
C: Uridylate kinase
hetero molecules

A: Uridylate kinase
C: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,43415
Polymers157,7436
Non-polymers6919
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
MethodPQS
2
B: Uridylate kinase
hetero molecules

B: Uridylate kinase
hetero molecules

B: Uridylate kinase
hetero molecules

B: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5308
Polymers105,1624
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
3
A: Uridylate kinase
C: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8115
Polymers52,5812
Non-polymers2303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-27 kcal/mol
Surface area19370 Å2
MethodPISA
4
B: Uridylate kinase
hetero molecules

B: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7654
Polymers52,5812
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area3410 Å2
ΔGint-28 kcal/mol
Surface area19470 Å2
MethodPISA
5
B: Uridylate kinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)158,29512
Polymers157,7436
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)158.292, 158.292, 58.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsHexamer. Hexamer is generated by crystallographic 3-fold symmetry.

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Components

#1: Protein Uridylate kinase / UK / Uridine monophosphate kinase / UMP kinase


Mass: 26290.486 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: pyrH / Production host: Escherichia coli (E. coli)
References: UniProt: P65932, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 55.2 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, Sodium Formate, Glycerol, KCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2004 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 27369 / Num. obs: 27369 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.118 / Net I/σ(I): 10.2
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 4.9 % / Num. unique all: 2381 / Rsym value: 0.632 / % possible all: 87.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→47.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 106236.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1247 4.9 %RANDOM
Rwork0.206 ---
obs0.206 25440 96.9 %-
all-25440 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.9512 Å2 / ksol: 0.318831 e/Å3
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å23.72 Å20 Å2
2---3.07 Å20 Å2
3---6.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5313 0 21 112 5446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 205 5.3 %
Rwork0.306 3644 -
obs-3644 89.2 %

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