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- PDB-4ggb: Crystal structure of a proposed galactarolactone cycloisomerase f... -

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Basic information

Entry
Database: PDB / ID: 4ggb
TitleCrystal structure of a proposed galactarolactone cycloisomerase from agrobacterium tumefaciens, TARGET EFI-500704, WITH BOUND CA, DISORDERED LOOPS
ComponentsPutative uncharacterized protein
KeywordsISOMERASE / ENOLASE / proposed galactarolactone cycloisomerase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


D-galactarolactone cycloisomerase / amino acid catabolic process / hydro-lyase activity / isomerase activity / magnesium ion binding
Similarity search - Function
D-galactarolactone cycloisomerase / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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 ...D-galactarolactone cycloisomerase / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / 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
D-galactarolactone cycloisomerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: Acta Crystallogr.,Sect.F / Year: 2016
Title: Purification, crystallization and structural elucidation of D-galactaro-1,4-lactone cycloisomerase from Agrobacterium tumefaciens involved in pectin degradation.
Authors: Vetting, M.W. / Bouvier, J.T. / Gerlt, J.A. / Almo, S.C.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Sep 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_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_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.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.pdbx_dist_value / _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_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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8029
Polymers41,5041
Non-polymers2978
Water3,315184
1
A: Putative uncharacterized protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)334,41372
Polymers332,0338
Non-polymers2,38064
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_595-x,-y+4,z1
crystal symmetry operation3_775-y+2,x+2,z1
crystal symmetry operation4_375y-2,-x+2,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_596x,-y+4,-z+11
crystal symmetry operation7_376y-2,x+2,-z+11
crystal symmetry operation8_776-y+2,-x+2,-z+11
Buried area38450 Å2
ΔGint-726 kcal/mol
Surface area83030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.178, 132.178, 95.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-406-

CL

21A-502-

HOH

31A-557-

HOH

41A-574-

HOH

51A-616-

HOH

61A-664-

HOH

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Components

#1: Protein Putative uncharacterized protein


Mass: 41504.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: Atu3139 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CEQ8
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 7.5
Details: Protein (10 mM Tris pH 7.9, 150 mM NaCl, 5 mM MgCl); Reservoir (0.2M CaCl2, 0.1 M Hepes pH 7.5, 28% Peg400); Cryoprotection (Reservoir), sitting drop vapor diffuction, temperature 298K

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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: 2→50 Å / Num. all: 28641 / Num. obs: 28641 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4128 / Rsym value: 0.68 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SJN

3sjn


Resolution: 2→38.697 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.813 / SU ML: 0.24 / σ(F): 0 / σ(I): 0 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1446 5.09 %RANDOM
Rwork0.1957 ---
all0.1976 28345 --
obs0.1976 28435 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.05 Å2 / Biso mean: 22.0495 Å2 / Biso min: 5.26 Å2
Refinement stepCycle: LAST / Resolution: 2→38.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 8 184 2856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122749
X-RAY DIFFRACTIONf_angle_d1.1513750
X-RAY DIFFRACTIONf_chiral_restr0.075409
X-RAY DIFFRACTIONf_plane_restr0.004489
X-RAY DIFFRACTIONf_dihedral_angle_d13.952991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07150.32931390.25012675281499
2.0715-2.15440.24761300.230927022832100
2.1544-2.25250.28361570.224426772834100
2.2525-2.37120.26221450.209826982843100
2.3712-2.51970.32291340.21327092843100
2.5197-2.71430.29491410.21622698283999
2.7143-2.98730.25851440.20792675281998
2.9873-3.41940.25371640.19672635279997
3.4194-4.30710.19771400.16932699283997
4.3071-38.70440.1741520.1772821297397
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)
12.9387-0.8265-0.62593.16490.65692.5962-0.021-0.1211-0.25930.1706-0.0047-0.33450.08060.21550.01010.12010.05250.01460.10030.01780.145718.6036225.487450.4124
20.984-0.21480.08960.3162-0.57970.6626-0.0449-0.0849-0.05870.0528-0.02610.14370.1388-0.00720.06920.12790.03990.04360.0944-0.03180.16028.217226.186843.9231
30.99620.64820.3733.35520.57881.4047-0.00880.3311-0.0815-0.6424-0.0672-0.22790.07250.25740.03460.26130.04910.05910.2063-0.02370.116414.0651245.99519.7135
40.56570.6729-0.48743.1443-2.60132.22620.0881-0.0001-0.0135-0.0213-0.1181-0.0941-0.05310.08610.02730.11060.02340.03540.0923-0.03020.10438.1786245.321539.2297
50.1111-0.42510.21820.8144-0.41651.3318-0.010.09490.1534-0.2269-0.0182-0.23330.06670.2244-0.00340.17870.01510.06610.1419-0.04040.19188.0754232.639830.6214
62.2809-0.93580.21091.7263-0.96271.0910.301-0.1021-1.1099-0.1264-0.27310.06730.50720.6997-0.04850.24110.08460.0886-0.0786-0.29980.248715.1598219.423931.6456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 127 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 227 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 228 through 288 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 289 through 341 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 342 through 374 )A0

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