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- PDB-3dfy: Crystal structure of apo dipeptide epimerase from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3dfy
TitleCrystal structure of apo dipeptide epimerase from Thermotoga maritima
ComponentsMuconate cycloisomerase
KeywordsISOMERASE / dipeptide epimerase / Thermotoga maritima / enzymatic function
Function / homology
Function and homology information


L-Ala-D/L-Glu epimerase / L-Ala-D/L-Glu epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / cell wall organization / cell wall macromolecule catabolic process / metal ion binding
Similarity search - Function
: / Dipeptide epimerase / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain ...: / Dipeptide epimerase / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-Ala-D/L-Glu epimerase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Structure / Year: 2008
Title: Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
Authors: Kalyanaraman, C. / Imker, H.J. / Fedorov, A.A. / Fedorov, E.V. / Glasner, M.E. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Muconate cycloisomerase
B: Muconate cycloisomerase
C: Muconate cycloisomerase
D: Muconate cycloisomerase
E: Muconate cycloisomerase
F: Muconate cycloisomerase
G: Muconate cycloisomerase
H: Muconate cycloisomerase
I: Muconate cycloisomerase
J: Muconate cycloisomerase
K: Muconate cycloisomerase
L: Muconate cycloisomerase
M: Muconate cycloisomerase
N: Muconate cycloisomerase
O: Muconate cycloisomerase
P: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)619,86532
Polymers619,47716
Non-polymers38916
Water19,3121072
1
A: Muconate cycloisomerase
B: Muconate cycloisomerase
C: Muconate cycloisomerase
D: Muconate cycloisomerase
E: Muconate cycloisomerase
F: Muconate cycloisomerase
G: Muconate cycloisomerase
H: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,93316
Polymers309,7388
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24320 Å2
ΔGint-97 kcal/mol
Surface area89760 Å2
MethodPISA
2
I: Muconate cycloisomerase
J: Muconate cycloisomerase
K: Muconate cycloisomerase
L: Muconate cycloisomerase
M: Muconate cycloisomerase
N: Muconate cycloisomerase
O: Muconate cycloisomerase
P: Muconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,93316
Polymers309,7388
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24160 Å2
ΔGint-101.8 kcal/mol
Surface area89330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.808, 165.142, 209.641
Angle α, β, γ (deg.)90.00, 96.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Muconate cycloisomerase


Mass: 38717.285 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXM1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1072 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 6000, 5% MPD, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 407187 / Num. obs: 407187 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TKK

1tkk


Resolution: 2.1→25 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1381048.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 20322 5 %RANDOM
Rwork0.246 ---
all0.246 407187 --
obs0.246 407187 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5306 Å2 / ksol: 0.37746 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1--11.69 Å20 Å2-0.97 Å2
2--19 Å20 Å2
3----7.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42027 0 16 1072 43115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.384 1970 4.9 %
Rwork0.362 38580 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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