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- PDB-3czx: The crystal structure of the putative N-acetylmuramoyl-L-alanine ... -

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Basic information

Entry
Database: PDB / ID: 3czx
TitleThe crystal structure of the putative N-acetylmuramoyl-L-alanine amidase from Neisseria meningitidis
ComponentsPutative N-acetylmuramoyl-L-alanine amidase
KeywordsHYDROLASE / N-acetylmuramoyl-L-alanine amidase / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesNeisseria meningitidis MC58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Zhou, M. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the putative N-acetylmuramoyl-L-alanine amidase from Neisseria meningitidis.
Authors: Zhang, R. / Zhou, M. / Bargassa, M. / Joachimiak, A.
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative N-acetylmuramoyl-L-alanine amidase
B: Putative N-acetylmuramoyl-L-alanine amidase
C: Putative N-acetylmuramoyl-L-alanine amidase
D: Putative N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6298
Polymers78,3674
Non-polymers2624
Water14,358797
1
A: Putative N-acetylmuramoyl-L-alanine amidase
B: Putative N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3144
Polymers39,1832
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative N-acetylmuramoyl-L-alanine amidase
D: Putative N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3144
Polymers39,1832
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6572
Polymers19,5921
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Putative N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6572
Polymers19,5921
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Putative N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6572
Polymers19,5921
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Putative N-acetylmuramoyl-L-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6572
Polymers19,5921
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.955, 65.039, 79.319
Angle α, β, γ (deg.)90.00, 109.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative N-acetylmuramoyl-L-alanine amidase /


Mass: 19591.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Strain: MC58 / Serogroup B / Gene: GI:7226323, NMB1085 / Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9JZE9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M Na/K phosphate pH 6.2, 10% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→74.74 Å / Num. all: 81655 / Num. obs: 78552 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.08
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.55 / Num. unique all: 6302 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→74.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.699 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21779 4146 5 %RANDOM
Rwork0.18011 ---
all0.18201 78552 --
obs0.18201 78552 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.763 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å21.01 Å2
2---0.8 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.6→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5429 0 4 797 6230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225514
X-RAY DIFFRACTIONr_bond_other_d0.0010.023740
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9477442
X-RAY DIFFRACTIONr_angle_other_deg0.93339135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94924.286224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57415954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7241536
X-RAY DIFFRACTIONr_chiral_restr0.090.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021084
X-RAY DIFFRACTIONr_nbd_refined0.220.21195
X-RAY DIFFRACTIONr_nbd_other0.2010.24044
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22784
X-RAY DIFFRACTIONr_nbtor_other0.0840.22883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2559
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.254
X-RAY DIFFRACTIONr_mcbond_it1.3221.54398
X-RAY DIFFRACTIONr_mcbond_other0.2751.51502
X-RAY DIFFRACTIONr_mcangle_it1.48725684
X-RAY DIFFRACTIONr_scbond_it2.64732184
X-RAY DIFFRACTIONr_scangle_it3.5994.51758
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 250 -
Rwork0.206 5233 -
obs-5483 87 %

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