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- PDB-4gfi: Crystal structure of EFI-502318, an enolase family member from Ag... -

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Entry
Database: PDB / ID: 4gfi
TitleCrystal structure of EFI-502318, an enolase family member from Agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, L-Ala-L-Glu with ordered loop)
ComponentsMandelate racemase/muconate lactonizing enzyme family protein
KeywordsISOMERASE / putative L-ALA-L/D-GLU epimerase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / 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 / Enolase-like, N-terminal ...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
ALANINE / GLUTAMIC ACID / Dipeptide epimerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVetting, M.W. / Bouvier, J.T. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of EFI-502318, an enolase family member from Agrobacterium tumefaciens with homology to dipeptide epimerases (bound sodium, l-ala-l-glu with ordered loop)
Authors: Vetting, M.W. / Bouvier, J.T. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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: Mandelate racemase/muconate lactonizing enzyme family protein
B: Mandelate racemase/muconate lactonizing enzyme family protein
C: Mandelate racemase/muconate lactonizing enzyme family protein
D: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,91926
Polymers141,2294
Non-polymers1,69022
Water12,629701
1
A: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5664
Polymers35,3071
Non-polymers2593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9229
Polymers35,3071
Non-polymers6148
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6986
Polymers35,3071
Non-polymers3915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mandelate racemase/muconate lactonizing enzyme family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7337
Polymers35,3071
Non-polymers4266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.901, 77.274, 215.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Mandelate racemase/muconate lactonizing enzyme family protein


Mass: 35307.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: Atu1648 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CIT6

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Non-polymers , 7 types, 723 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM Tris pH 7.5, 5 mM MgCl, 50 mM L-Ala,L-Glu), Reservoir (0.1 M HEPES:NaOH pH 7.5, 2.0 M Ammonium Sulfate), Cryoprotection (Drop was superconcentrated, no added cryoprotection ...Details: Protein (10 mM Tris pH 7.5, 5 mM MgCl, 50 mM L-Ala,L-Glu), Reservoir (0.1 M HEPES:NaOH pH 7.5, 2.0 M Ammonium Sulfate), Cryoprotection (Drop was superconcentrated, no added cryoprotection required), sitting drop vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 9, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→107.912 Å / Num. all: 102243 / Num. obs: 102243 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 17.2
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.737 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPD

1jpd


Resolution: 1.9→62.827 Å / Occupancy max: 1 / Occupancy min: 0.02 / FOM work R set: 0.8573 / SU ML: 0.2 / σ(F): 0 / σ(I): 0 / Phase error: 21.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 5097 4.99 %RANDOM
Rwork0.171 ---
all0.1731 102114 --
obs0.1731 102114 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.01 Å2 / Biso mean: 22.6225 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→62.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9789 0 95 701 10585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810131
X-RAY DIFFRACTIONf_angle_d1.08713798
X-RAY DIFFRACTIONf_chiral_restr0.0711586
X-RAY DIFFRACTIONf_plane_restr0.0051816
X-RAY DIFFRACTIONf_dihedral_angle_d13.6383759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.28611560.222332643420100
1.9216-1.94420.29981620.219231953357100
1.9442-1.96790.29241910.207431423333100
1.9679-1.99280.26981530.20332063359100
1.9928-2.0190.22961810.198432053386100
2.019-2.04670.2771800.197831893369100
2.0467-2.0760.27411440.194332213365100
2.076-2.10690.26051710.19331773348100
2.1069-2.13990.25171750.183232423417100
2.1399-2.17490.23871730.179131603333100
2.1749-2.21250.25431520.183232383390100
2.2125-2.25270.2121690.172831523321100
2.2527-2.2960.24171680.176932383406100
2.296-2.34290.23221650.178132213386100
2.3429-2.39380.24961580.18132263384100
2.3938-2.44950.22821790.178431663345100
2.4495-2.51080.23851630.184732353398100
2.5108-2.57870.23171630.182732593422100
2.5787-2.65450.22251920.183232093401100
2.6545-2.74020.21651830.178632023385100
2.7402-2.83820.21911670.181532153382100
2.8382-2.95180.23341810.190832423423100
2.9518-3.08610.24551830.189432313414100
3.0861-3.24880.20661680.180132443412100
3.2488-3.45240.20531580.16732593417100
3.4524-3.71890.18271600.156232743434100
3.7189-4.09310.17971620.143133173479100
4.0931-4.68520.16791830.134632783461100
4.6852-5.90220.17871710.149833603531100
5.9022-62.86140.17091860.16063450363699
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)
10.6428-0.0137-0.30910.69680.07550.9652-0.0229-0.21490.03990.0958-0.06220.0572-0.2398-0.14660.08150.1940.0756-0.02010.38620.02930.1745-17.57669.78011.3296
21.2699-0.4020.31771.018-0.52041.1158-0.09730.06710.0446-0.1869-0.1216-0.0466-0.00850.05680.12110.3113-0.033-0.07430.17410.02560.1253-11.75599.4757-22.9288
30.20560.1854-0.02690.1863-0.19691.5158-0.1028-0.09360.142-0.08770.02360.1355-0.2221-0.18320.05960.19990.0685-0.0640.3501-0.00510.1495-25.24398.5246-12.0496
40.8442-0.2168-0.36970.6399-0.36780.8826-0.0642-0.180.01470.0935-0.017-0.0513-0.04780.0090.03920.11350.0719-0.02790.36470.05010.0975-15.3267-0.17912.9267
50.58730.34670.18280.7812-0.15320.258-0.03350.0803-0.1936-0.10990.0122-0.16730.07960.065-0.01860.1875-0.01980.09830.0221-0.00840.26919.663-13.2178-58.535
60.40420.20490.08390.45130.04130.3714-0.0108-0.0515-0.0130.0349-0.0362-0.0146-0.04450.01890.02550.1234-0.01210.0210.04680.02470.16269.41694.3987-46.1132
70.17970.1682-0.16310.7898-0.20520.15540.0752-0.0676-0.08310.1276-0.0793-0.14580.10850.0696-0.01830.1603-0.0366-0.03970.49220.31750.3964-10.2288-36.23765.5139
80.53510.125-0.03650.23010.07230.2161-0.0277-0.2117-0.11210.0303-0.0709-0.15670.08080.09130.0150.0023-0.03640.03110.47610.22920.2842-16.0864-28.79390.2039
90.94580.3341-0.45371.1596-0.1431.2219-0.0537-0.0229-0.0122-0.1331-0.0118-0.09510.05470.04380.02640.1260.01210.04510.25910.09970.1865-24.0493-30.4585-19.1851
100.53920.05890.09890.16260.06110.08-0.0218-0.1682-0.06860.0122-0.0503-0.00850.0204-0.0396-0.0171-0.011-0.05150.04360.45960.19090.1996-20.4012-24.6582-0.8483
110.90630.0436-0.05920.5402-0.11140.7514-0.01480.13130.1642-0.07750.00390.0395-0.1004-0.16120.00580.17810.0291-0.03180.09970.01580.1469-30.63394.0221-60.7701
121.0842-0.1487-0.24511.36070.29880.9335-0.0195-0.2222-0.02680.0262-0.08810.0174-0.0291-0.07550.09590.0946-0.00410.00620.1402-0.00480.0805-27.5427-10.0918-35.6719
130.79440.0281-0.1210.5518-0.27140.7341-0.0441-0.03770.06220.0496-0.0511-0.0389-0.0281-0.0430.08640.1390.0177-0.010.0602-0.01010.09-22.64120.4187-50.8691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 166 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 218 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 278 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 279 through 327 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 104 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 105 through 327 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 37 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 38 through 166 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 167 through 236 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 237 through 327 )C0
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 123 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 124 through 236 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 237 through 403 )D0

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