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- PDB-1j6u: Crystal structure of UDP-N-acetylmuramate-alanine ligase MurC (TM... -

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Basic information

Entry
Database: PDB / ID: 1j6u
TitleCrystal structure of UDP-N-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution
ComponentsUDP-N-acetylmuramate-alanine ligase MurC
KeywordsLIGASE / STRUCTURAL GENOMICS / TM0231 / UDP-N-acetylmuramate-alanine ligase MurC / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily ...UDP-N-acetylmuramate--L-alanine ligase / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution.
Authors: Spraggon, G. / Schwarzenbacher, R. / Kreusch, A. / Lee, C.C. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / ...Authors: Spraggon, G. / Schwarzenbacher, R. / Kreusch, A. / Lee, C.C. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kuhn, P. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Lesley, S.A. / Wilson, I.A.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylmuramate-alanine ligase MurC


Theoretical massNumber of molelcules
Total (without water)53,8271
Polymers53,8271
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.11, 244.11, 244.11
Angle α, β, γ (deg.)90, 90, 90
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

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Components

#1: Protein UDP-N-acetylmuramate-alanine ligase MurC / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 53827.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0231 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WY73, UDP-N-acetylmuramate-L-alanine ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 5.58 Å3/Da / Density % sol: 78.82 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 1.4M sodium potassium phosphate ph 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 7.50
Crystal grow
*PLUS
Method: other
Details: Santarsiero, B.D., (2002) J. Appl. Crystallogr., 35, 278.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2002
RadiationMonochromator: ASYMMETRICALLY CUT SI CRYSTAL, CYLINDRICALLY BENT
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→182 Å / Num. obs: 52273 / % possible obs: 95.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 55.2 Å2 / Rsym value: 0.099 / Net I/σ(I): 9.55
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.96 / Rsym value: 0.77 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 70.71 Å / Num. obs: 54912 / % possible obs: 97.7 % / Redundancy: 4.3 % / Num. measured all: 252363 / Rmerge(I) obs: 0.124
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 96.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOSFLMdata reduction
CCP4data reduction
SCALEPACKdata scaling
SnBphasing
MLPHAREphasing
CCP4model building
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.6 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2639 4.8 %RANDOM
Rwork0.234 ---
obs0.234 52273 95.3 %-
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 0.4 Å2 / ksol: 89.02 e/Å3
Displacement parametersBiso mean: 49.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 0 245 3694
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.77
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.2681.5
X-RAY DIFFRACTIONc_mcangle_it6.7442
X-RAY DIFFRACTIONc_scbond_it8.8682
X-RAY DIFFRACTIONc_scangle_it11.0722.5
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.442 31 3.2 %
Rwork0.388 981 -
obs--94.7 %
Refinement
*PLUS
Num. reflection obs: 54912
Solvent computation
*PLUS
Displacement parameters
*PLUS

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