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- PDB-4xxt: Crystal structure of Fused Zn-dependent amidase/peptidase/peptodo... -

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Basic information

Entry
Database: PDB / ID: 4xxt
TitleCrystal structure of Fused Zn-dependent amidase/peptidase/peptodoglycan-binding domain-containing protein from Clostridium acetobutylicum ATCC 824
ComponentsFusion of predicted Zn-dependent amidase/peptidase (Cell wall hydrolase/DD-carboxypeptidase family) and uncharacterized domain of ErfK family peptodoglycan-binding domain
KeywordsHYDROLASE / L / D-transpeptidases / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peptidoglycan biosynthetic process / carboxypeptidase activity / transferase activity
Similarity search - Function
PGBD superfamily / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Fusion of predicted Zn-dependent amidase/peptidase (Cell wall hydrolase/DD-carboxypeptidase family) and uncharacterized domain of ErfK family peptodoglycan-binding domain
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsChang, C. / Cuff, M. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of Fused Zn-dependent amidase/peptidase/peptodoglycan-binding domain-containing protein from from Clostridium acetobutylicum ATCC 824
Authors: Chang, C. / Cuff, M. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJan 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion of predicted Zn-dependent amidase/peptidase (Cell wall hydrolase/DD-carboxypeptidase family) and uncharacterized domain of ErfK family peptodoglycan-binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4047
Polymers29,0201
Non-polymers3836
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.790, 60.790, 125.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-482-

HOH

21A-485-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Fusion of predicted Zn-dependent amidase/peptidase (Cell wall hydrolase/DD-carboxypeptidase family) and uncharacterized domain of ErfK family peptodoglycan-binding domain


Mass: 29020.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: CA_C1822 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q97I32
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Calcium Acetate, 0.1M Tris-HCl, 20% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 20, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 26936 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.015 / Rrim(I) all: 0.044 / Χ2: 0.856 / Net I/av σ(I): 45.293 / Net I/σ(I): 13.5 / Num. measured all: 219308
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.860.5052.8412260.9110.2180.5520.8193.4
1.8-1.837.10.50413320.9350.2020.5440.792100
1.83-1.877.70.39313010.9610.1510.4210.763100
1.87-1.918.40.31113650.980.1140.3310.819100
1.91-1.958.40.24113220.9830.0880.2570.819100
1.95-1.998.50.1913140.9890.0690.2020.823100
1.99-2.048.40.16313450.9920.0590.1740.855100
2.04-2.18.50.13313380.9960.0490.1420.869100
2.1-2.168.50.1113340.9950.040.1170.899100
2.16-2.238.50.09513280.9950.0350.1020.904100
2.23-2.318.40.08413350.9970.0310.090.924100
2.31-2.48.50.07413600.9970.0270.0790.913100
2.4-2.518.50.06413450.9970.0230.0680.877100
2.51-2.648.40.05313610.9980.0190.0570.896100
2.64-2.818.40.04313330.9980.0150.0450.879100
2.81-3.038.40.03313670.9990.0120.0350.828100
3.03-3.338.30.02913600.9990.010.0310.823100
3.33-3.818.30.02513960.9990.0090.0270.858100
3.81-4.88.10.02414030.9990.0090.0260.824100
4.8-507.40.02714710.9980.0110.0290.91698.1

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Processing

Software
NameVersionClassification
HKL-3000data reduction
SBC-Collectdata collection
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→27.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.156 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1334 5 %RANDOM
Rwork0.1676 25217 --
obs0.169 25217 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.62 Å2 / Biso mean: 26.48 Å2 / Biso min: 12.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 1.77→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1707 0 26 223 1956
Biso mean--56.04 36.01 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191879
X-RAY DIFFRACTIONr_bond_other_d0.0010.021732
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9472560
X-RAY DIFFRACTIONr_angle_other_deg0.71633985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3785242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08925.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62715287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.816156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212236
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
X-RAY DIFFRACTIONr_mcbond_it0.6991.214942
X-RAY DIFFRACTIONr_mcbond_other0.6941.212940
X-RAY DIFFRACTIONr_mcangle_it1.2791.7961192
LS refinement shellResolution: 1.771→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 95 -
Rwork0.222 1748 -
all-1843 -
obs--93.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9212-1.21910.8098.5535-2.94562.677-0.04940.00620.1382-0.11950.05220.6164-0.1234-0.166-0.00280.10530.0374-0.01610.1045-0.01160.1825-3.948940.67890.8981
28.60651.068-6.12535.04122.602312.4734-0.22050.3398-0.0997-0.11820.08530.27020.2743-0.31450.13520.03910.0329-0.00630.0954-0.00670.12171.852131.8378-0.585
32.0117-0.0780.24861.79430.57782.8952-0.05190.0872-0.03430.0810.02490.0897-0.0951-0.17260.0270.11010.04570.01380.06830.00260.13289.318934.58383.8037
43.1165-0.2721-0.51351.84040.52183.8473-0.04750.07170.1960.0213-0.00820.0311-0.5844-0.15290.05570.19760.0624-0.00210.02380.01080.12359.791345.67093.9267
55.4347-2.725.82.5694-2.68416.2378-0.24680.20940.29670.1259-0.0293-0.3137-0.29180.25850.2760.1365-0.03670.00410.1327-0.01030.155427.02736.308710.3533
66.48151.90150.427510.7218-1.53213.5795-0.2376-0.24630.0360.1926-0.0767-0.43720.01090.24290.31430.07280.0132-0.06580.1166-0.00760.105735.524829.199223.3499
70.9653-0.73740.35571.9648-0.34822.6174-0.1693-0.1193-0.07020.27240.1641-0.043-0.1260.06160.00520.15020.0755-0.00650.08190.01220.114222.242528.182423.3563
81.1729-1.16051.00412.4749-0.97183.1513-0.3122-0.2359-0.07010.39860.4120.1813-0.3824-0.388-0.09980.24690.15560.02990.1260.01030.107312.495736.213523.6926
96.3101-0.2352-8.47735.53397.093919.71240.23620.00540.2164-0.0445-0.08310.073-0.3807-0.1285-0.15310.24560.0842-0.07540.0528-0.08520.174318.569952.721529.9105
106.09692.14210.29514.01940.89511.7443-0.1789-0.26610.12760.37190.24470.073-0.4745-0.1014-0.06580.35720.1445-0.02650.1074-0.04280.107316.143343.365327.7871
111.35743.3857-1.51858.4736-3.73191.91440.2066-0.1662-0.0280.4985-0.4091-0.0349-0.37550.08430.20250.37110.0461-0.05820.1485-0.11330.168620.403447.706239.2253
121.6078-0.6420.57481.9208-0.44492.9814-0.3083-0.1120.07640.39720.3109-0.0507-0.522-0.0319-0.00250.28730.1034-0.02910.0713-0.0390.114119.947538.110223.8963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 58
2X-RAY DIFFRACTION2A59 - 67
3X-RAY DIFFRACTION3A68 - 97
4X-RAY DIFFRACTION4A98 - 124
5X-RAY DIFFRACTION5A125 - 136
6X-RAY DIFFRACTION6A137 - 142
7X-RAY DIFFRACTION7A143 - 198
8X-RAY DIFFRACTION8A199 - 212
9X-RAY DIFFRACTION9A213 - 222
10X-RAY DIFFRACTION10A223 - 243
11X-RAY DIFFRACTION11A244 - 254
12X-RAY DIFFRACTION12A255 - 281

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