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- PDB-1r8g: Structure and function of YbdK -

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Basic information

Entry
Database: PDB / ID: 1r8g
TitleStructure and function of YbdK
ComponentsHypothetical protein ybdK
KeywordsLIGASE / Structural Genomics / unknown function / YbdK / hypothetical protein / carboxylate-amine ligase / Structure 2 Function Project / S2F
Function / homology
Function and homology information


cellular modified amino acid biosynthetic process / glutamate-cysteine ligase / glutamate-cysteine ligase activity / ligase activity, forming carbon-nitrogen bonds / ATP binding
Similarity search - Function
Putative glutamate--cysteine ligase YbdK / Glutamate--cysteine ligase, GCS2 / Glutamate-cysteine ligase family 2(GCS2) / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative glutamate--cysteine ligase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsLehmann, C. / Doseeva, V. / Pullalarevu, S. / Krajewski, W. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004
Title: YbdK is a carboxylate-amine ligase with a gamma-glutamyl:Cysteine ligase activity: crystal structure and enzymatic assays
Authors: Lehmann, C. / Doseeva, V. / Pullalarevu, S. / Krajewski, W. / Howard, A. / Herzberg, O.
History
DepositionOct 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 28, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_conn / struct_ref_seq_dif
Item: _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs ..._refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein ybdK
B: Hypothetical protein ybdK


Theoretical massNumber of molelcules
Total (without water)84,5062
Polymers84,5062
Non-polymers00
Water11,818656
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-24 kcal/mol
Surface area28110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.47, 100.32, 71.37
Angle α, β, γ (deg.)90.00, 99.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hypothetical protein ybdK


Mass: 42253.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBDK, B0581 / Plasmid: PET100-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: P77213, EC: 6.3.-.-
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NaCl, 20% w/v PEG 3350, 20mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2003 / Details: Mirror
RadiationMonochromator: Cryogenically-cooled Si(111) double crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.15→29.86 Å / Num. all: 62133 / Num. obs: 62133 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.055 / Net I/σ(I): 15.34
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 0.9 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 6.71 / Num. unique all: 1142 / Rsym value: 0.128 / % possible all: 49.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RESOLVEmodel building
CNS1refinement
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1766 2.88 %Random
Rwork0.189 ---
all-61334 --
obs-61334 83.6 %-
Displacement parametersBiso mean: 22.1 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5578 0 0 656 6234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.47
LS refinement shellResolution: 2.15→2.17 Å /
RfactorNum. reflection
Rfree0.394 16
Rwork0.246 -
obs-691

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