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- PDB-3tkk: Crystal Structure Analysis of a recombinant predicted acetamidase... -

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Basic information

Entry
Database: PDB / ID: 3tkk
TitleCrystal Structure Analysis of a recombinant predicted acetamidase/ formamidase from the thermophile thermoanaerobacter tengcongensis
ComponentsPredicted acetamidase/formamidase
KeywordsHYDROLASE / Beta/Alpha structure
Function / homologyAcetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Predicted acetamidase/formamidase
Function and homology information
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsQian, M. / Huang, Q. / Wu, G. / Lai, L. / Tang, Y. / Pei, J. / Kusunoki, M.
CitationJournal: PROTEIN J. / Year: 2012
Title: Crystal Structure Analysis of a Recombinant Predicted Acetamidase/Formamidase from the Thermophile Thermoanaerobacter tengcongensis.
Authors: Qian, M. / Huang, Q. / Wu, G. / Lai, L. / Tang, Y. / Pei, J. / Kusunoki, M.
History
DepositionAug 26, 2011Deposition site: RCSB / Processing site: PDBJ
SupersessionNov 16, 2011ID: 3MJJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted acetamidase/formamidase
B: Predicted acetamidase/formamidase
C: Predicted acetamidase/formamidase
D: Predicted acetamidase/formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,15013
Polymers128,6884
Non-polymers4629
Water15,043835
1
A: Predicted acetamidase/formamidase
C: Predicted acetamidase/formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5957
Polymers64,3442
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-86 kcal/mol
Surface area22400 Å2
MethodPISA
2
B: Predicted acetamidase/formamidase
D: Predicted acetamidase/formamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5556
Polymers64,3442
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-107 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.230, 152.882, 100.255
Angle α, β, γ (deg.)90.00, 99.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A-2 - 299
2114B-2 - 299
3114C-2 - 299
4114D-2 - 299

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Components

#1: Protein
Predicted acetamidase/formamidase


Mass: 32171.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4T / Gene: TTE1919 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA DE3 / References: UniProt: Q8R8S5
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 835 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M calcium acetate, 0.1M sodium cacodylate, 18%(W/V) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 4, 2004 / Details: mirrors
RadiationMonochromator: DOUBLE MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→99.01 Å / Num. all: 81396 / Num. obs: 75255 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.8
Reflection shellResolution: 2→2.04 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3778 / % possible all: 64.62

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.99→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.291 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23682 3985 5 %RANDOM
Rwork0.17397 ---
all0.178 81396 --
obs0.17716 75255 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.712 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å22.57 Å2
2---2.15 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.99→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9028 0 9 835 9872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0229209
X-RAY DIFFRACTIONr_angle_refined_deg2.2371.97912392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86151196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34126.512344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.637151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2871512
X-RAY DIFFRACTIONr_chiral_restr0.1760.21464
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216664
X-RAY DIFFRACTIONr_mcbond_it1.60225958
X-RAY DIFFRACTIONr_mcangle_it2.46739552
X-RAY DIFFRACTIONr_scbond_it2.32923251
X-RAY DIFFRACTIONr_scangle_it3.38332840
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2257 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.550.5
Bmedium positional0.610.5
Cmedium positional0.50.5
Dmedium positional0.570.5
Amedium thermal1.852
Bmedium thermal1.22
Cmedium thermal1.52
Dmedium thermal1.282
LS refinement shellResolution: 1.99→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 219 -
Rwork0.242 3778 -
obs-3778 64.62 %
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)
10.7855-0.2056-0.46682.75030.57651.0236-0.01490.0421-0.1547-0.1758-0.0151-0.0372-0.0063-0.04960.030.07450.0073-0.07640.1824-0.01160.27394.62119.5090.785
20.82190.2141-0.22421.9124-0.80941.4945-0.081-0.0946-0.19070.12310.13270.04790.199-0.0997-0.05170.48770.02780.1320.23020.02640.3781-23.41612.57549.438
30.5361-0.6241-0.15713.10680.25990.13460.14140.04260.1682-0.3956-0.037-0.1862-0.2038-0.025-0.10430.28740.0063-0.00070.18050.01030.28282.08451.9564.062
40.8766-0.3368-0.05252.30710.3530.984-0.0844-0.12290.2120.17110.1104-0.013-0.3062-0.0003-0.0260.59290.05440.11480.2393-0.04390.3872-24.17244.64951.888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 299
2X-RAY DIFFRACTION2B1 - 299
3X-RAY DIFFRACTION3C1 - 299
4X-RAY DIFFRACTION4D1 - 299

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