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- PDB-3kxp: Crystal Structure of E-2-(Acetamidomethylene)succinate Hydrolase -

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Basic information

Entry
Database: PDB / ID: 3kxp
TitleCrystal Structure of E-2-(Acetamidomethylene)succinate Hydrolase
ComponentsAlpha-(N-acetylaminomethylene)succinic acid hydrolase
KeywordsHYDROLASE / alpha/beta hydrolase / PLP degradation / E-2-(acetamidomethylene)succinate
Function / homology
Function and homology information


2-(acetamidomethylene)succinate hydrolase / 2-(acetamidomethylene)succinate hydrolase activity / vitamin B6 catabolic process / protein homodimerization activity
Similarity search - Function
: / Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(acetamidomethylene)succinate hydrolase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsMcCulloch, K.M. / Mukherjee, T. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2010
Title: Structure determination and characterization of the vitamin B(6) degradative enzyme (E)-2-(acetamidomethylene)succinate hydrolase.
Authors: McCulloch, K.M. / Mukherjee, T. / Begley, T.P. / Ealick, S.E.
History
DepositionDec 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
A: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
B: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
C: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
D: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
E: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
F: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
G: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
H: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
I: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
J: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
K: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
L: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)410,28224
Polymers409,85712
Non-polymers42512
Water24,9871387
1
A: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
L: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3804
Polymers68,3092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-34 kcal/mol
Surface area19800 Å2
MethodPISA
2
B: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
C: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3804
Polymers68,3092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-36 kcal/mol
Surface area19970 Å2
MethodPISA
3
D: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
E: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3804
Polymers68,3092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-35 kcal/mol
Surface area20040 Å2
MethodPISA
4
F: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
G: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3804
Polymers68,3092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-36 kcal/mol
Surface area20110 Å2
MethodPISA
5
H: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
J: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3804
Polymers68,3092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-36 kcal/mol
Surface area19850 Å2
MethodPISA
6
I: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
K: Alpha-(N-acetylaminomethylene)succinic acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3804
Polymers68,3092
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-35 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.200, 178.530, 189.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Alpha-(N-acetylaminomethylene)succinic acid hydrolase / E-2-(Acetamidomethylene)succinate Hydrolase


Mass: 34154.715 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: 5331 / Plasmid: XF1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q988D4
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1387 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.3748.19THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, hanging drop7.58-12% PEG8000, 200 mM MgCl2, 100 mM Tris, pH 7.5, vapor diffusion, hanging drop, temperature 295K
2952vapor diffusion, hanging drop, microseeding7.59% PEG8000, 200 mM MgCl2, 100 mM Tris, pH 7.5, vapor diffusion, hanging drop, microseeding, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9792
SYNCHROTRONAPS 24-ID-E20.97883
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 18, 2008
ADSC QUANTUM 3152CCDFeb 22, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.978831
ReflectionResolution: 2.26→50 Å / Num. obs: 297847 / % possible obs: 91.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.103 / Χ2: 2.811 / Net I/av σ(I): 13.056 / Net I/σ(I): 7 / Num. measured all: 727191
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.26-2.342.10.458124410.74868.2
2.34-2.433.20.435157480.67386.3
2.43-2.5540.37170990.65793.6
2.55-2.684.50.288176330.81896.2
2.68-2.854.70.211177161.0696.8
2.85-3.074.70.16177411.29896.8
3.07-3.384.80.121177181.48496.2
3.38-3.864.80.091176531.41395.5
3.86-4.874.80.066175241.2494.4
4.87-504.80.0461749515.48891.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.26→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.245 18821 5.6 %
Rwork0.204 --
obs-297847 88.9 %
Solvent computationBsol: 33.239 Å2
Displacement parametersBiso max: 98.6 Å2 / Biso mean: 33.906 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.786 Å20 Å20 Å2
2--10.712 Å20 Å2
3----12.498 Å2
Refinement stepCycle: LAST / Resolution: 2.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24432 0 12 1387 25831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.246
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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