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- PDB-3ne8: The crystal structure of a domain from N-acetylmuramoyl-l-alanine... -

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Basic information

Entry
Database: PDB / ID: 3ne8
TitleThe crystal structure of a domain from N-acetylmuramoyl-l-alanine amidase of Bartonella henselae str. Houston-1
ComponentsN-acetylmuramoyl-l-alanine amidase
KeywordsHYDROLASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
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 / membrane / metal ion binding
Similarity search - Function
Zn-dependent exopeptidases / : / Ami_3 / N-acetylmuramoyl-L-alanine amidase, catalytic domain / N-acetylmuramoyl-L-alanine amidase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.239 Å
AuthorsTan, K. / Rakowski, E. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Mol.Microbiol. / Year: 2012
Title: A conformational switch controls cell wall-remodelling enzymes required for bacterial cell division.
Authors: Yang, D.C. / Tan, K. / Joachimiak, A. / Bernhardt, T.G.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 7, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramoyl-l-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7349
Polymers26,1691
Non-polymers5658
Water4,612256
1
A: N-acetylmuramoyl-l-alanine amidase
hetero molecules

A: N-acetylmuramoyl-l-alanine amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,46818
Polymers52,3382
Non-polymers1,13016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5390 Å2
ΔGint-18 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.185, 53.511, 58.495
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetylmuramoyl-l-alanine amidase


Mass: 26169.201 Da / Num. of mol.: 1 / Fragment: sequence database residues 179-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Gene: amiB, BH08710 / Plasmid: pMCSG19B / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q6G3B2, UniProt: A0A0H3M3F4*PLUS

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Non-polymers , 5 types, 264 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FMT / FORMIC ACID


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


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane, 1.8M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.24→30 Å / Num. all: 61785 / Num. obs: 61785 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.2
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.52 / Num. unique all: 2765 / % possible all: 90.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.239→29.247 Å / SU ML: 0.14 / σ(F): 0.03 / σ(I): 0 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 2934 5.06 %random
Rwork0.1606 ---
obs0.1613 58025 93.03 %-
all-58025 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.489 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5271 Å2-0 Å21.0819 Å2
2--1.915 Å20 Å2
3----2.4421 Å2
Refinement stepCycle: LAST / Resolution: 1.239→29.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 34 256 2066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051969
X-RAY DIFFRACTIONf_angle_d0.9852684
X-RAY DIFFRACTIONf_dihedral_angle_d17.302771
X-RAY DIFFRACTIONf_chiral_restr0.068307
X-RAY DIFFRACTIONf_plane_restr0.005355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.239-1.28330.24392170.25594412X-RAY DIFFRACTION75
1.2833-1.33470.25762480.22494996X-RAY DIFFRACTION85
1.3347-1.39540.19382840.19915278X-RAY DIFFRACTION89
1.3954-1.4690.21442960.17575405X-RAY DIFFRACTION92
1.469-1.5610.19222890.15845625X-RAY DIFFRACTION95
1.561-1.68150.15643150.14345763X-RAY DIFFRACTION98
1.6815-1.85070.1613120.14825853X-RAY DIFFRACTION98
1.8507-2.11850.15663150.14645885X-RAY DIFFRACTION99
2.1185-2.66870.17793280.15545920X-RAY DIFFRACTION100
2.6687-29.25470.15363300.14995954X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.2425 Å / Origin y: 18.6636 Å / Origin z: 44.1104 Å
111213212223313233
T0.0826 Å2-0.0081 Å2-0.0045 Å2-0.0785 Å2-0.0053 Å2--0.0884 Å2
L0.5258 °20.0183 °2-0.1306 °2-0.4285 °2-0.082 °2--1.0646 °2
S-0.0241 Å °0.0201 Å °0.0132 Å °-0.0571 Å °0.0223 Å °0.0082 Å °0.0319 Å °-0.0549 Å °0.001 Å °
Refinement TLS groupSelection details: chain A

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