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- PDB-4l08: Crystal structure of the maleamate amidase Ami(C149A) in complex ... -

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Basic information

Entry
Database: PDB / ID: 4l08
TitleCrystal structure of the maleamate amidase Ami(C149A) in complex with maleate from Pseudomonas putida S16
ComponentsHydrolase, isochorismatase family
KeywordsHYDROLASE / maleamate amidase
Function / homology
Function and homology information


Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALEIC ACID / Hydrolase, isochorismatase family
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsChen, D.D. / Lu, Y. / Zhang, Z. / Wu, G. / Xu, P.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structural insights into the specific recognition of N-heterocycle biodenitrogenation-derived substrates by microbial amide hydrolases.
Authors: Wu, G. / Chen, D. / Tang, H. / Ren, Y. / Chen, Q. / Lv, Y. / Zhang, Z. / Zhao, Y.L. / Yao, Y. / Xu, P.
History
DepositionMay 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hydrolase, isochorismatase family
A: Hydrolase, isochorismatase family
C: Hydrolase, isochorismatase family
D: Hydrolase, isochorismatase family
E: Hydrolase, isochorismatase family
F: Hydrolase, isochorismatase family
G: Hydrolase, isochorismatase family
H: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,01716
Polymers177,0888
Non-polymers9298
Water905
1
B: Hydrolase, isochorismatase family
E: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-6 kcal/mol
Surface area15240 Å2
MethodPISA
2
A: Hydrolase, isochorismatase family
G: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-6 kcal/mol
Surface area15260 Å2
MethodPISA
3
C: Hydrolase, isochorismatase family
F: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-7 kcal/mol
Surface area15390 Å2
MethodPISA
4
D: Hydrolase, isochorismatase family
H: Hydrolase, isochorismatase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5044
Polymers44,2722
Non-polymers2322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-6 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.449, 167.045, 175.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Hydrolase, isochorismatase family / / Maleamate amidase


Mass: 22136.059 Da / Num. of mol.: 8 / Mutation: C149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: S16 / Gene: PPS_4057 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F8G0M0
#2: Chemical
ChemComp-MAE / MALEIC ACID / Maleic acid


Mass: 116.072 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.07 Å3/Da / Density % sol: 59.97 % / Mosaicity: 0.934 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M sodium citrate, pH 5.8, 19% polyethylene glycol monomethylether 5000, vapor diffusion, hanging drop, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→120.84 Å / Num. obs: 63356 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Χ2: 1.011 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.746.60.33962561.0571100
2.74-2.856.60.2762831.0221100
2.85-2.986.70.21362480.9691100
2.98-3.146.80.15862891.0291100
3.14-3.3470.133629411100
3.34-3.670.12163191.0611100
3.6-3.9670.11363461.021199.9
3.96-4.5370.08663390.993199.9
4.53-5.716.90.06664720.99199.9
5.71-506.80.05965100.969197.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 12.622 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.657 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 3195 5.1 %RANDOM
Rwork0.2221 ---
obs0.2237 62880 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.95 Å2 / Biso mean: 60.0688 Å2 / Biso min: 35.52 Å2
Baniso -1Baniso -2Baniso -3
1-6.08 Å20 Å20 Å2
2---2.09 Å20 Å2
3----3.99 Å2
Refinement stepCycle: LAST / Resolution: 2.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12255 0 64 5 12324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212559
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.96517109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4751640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32324.213470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61151931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6541556
X-RAY DIFFRACTIONr_chiral_restr0.0710.22016
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219472
LS refinement shellResolution: 2.658→2.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 222 -
Rwork0.415 3851 -
all-4073 -
obs--93.68 %

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