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

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Basic information

Entry
Database: PDB / ID: 4hpn
TitleCrystal structure of a proposed galactarolactone cycloisomerase from Agrobacterium Tumefaciens, target EFI-500704, with bound Ca, ordered loops
ComponentsPutative uncharacterized protein
KeywordsISOMERASE / ENOLASE / 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
IMIDAZOLE / NICKEL (II) ION / D-galactarolactone cycloisomerase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 F Struct Biol Commun / 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
DepositionOct 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 20, 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)41,7125
Polymers41,5041
Non-polymers2084
Water8,629479
1
A: Putative uncharacterized protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)333,69740
Polymers332,0338
Non-polymers1,66332
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area34270 Å2
ΔGint-307 kcal/mol
Surface area89090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.145, 121.145, 128.446
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-525-

HOH

21A-704-

HOH

31A-810-

HOH

41A-885-

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 / ATCC 33970 / 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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (10 mM Tris, pH 7.9, 150 mM NaCl, 50 mM MgCl), Reservoir (0.2 M Calcium Acetate, 0.1 M Imidazole:HCl, pH 8.0, 10% (w/v) PEG 8000), Cryoprotection (Reservoir + 20% glycerol), VAPOR ...Details: Protein (10 mM Tris, pH 7.9, 150 mM NaCl, 50 mM MgCl), Reservoir (0.2 M Calcium Acetate, 0.1 M Imidazole:HCl, pH 8.0, 10% (w/v) PEG 8000), Cryoprotection (Reservoir + 20% glycerol), VAPOR DIFFUSION, SITTING DROP, 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: Oct 16, 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: 1.6→88.131 Å / Num. all: 62863 / Num. obs: 62863 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.6914.50.8990.913159790780.899100
1.69-1.7914.50.631.212476585990.63100
1.79-1.9114.50.4261.811757180840.426100
1.91-2.0714.60.257311010475390.257100
2.07-2.2614.70.1933.810255369620.193100
2.26-2.5314.80.1624.39349963210.162100
2.53-2.9214.80.1265.38300256050.126100
2.92-3.5814.80.0738.67060347850.073100
3.58-5.0614.60.04215.15468237460.042100
5.06-25.69313.80.04114.32962721440.04199.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4GGB

4ggb


Resolution: 1.6→25.693 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.9199 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 14.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1609 3190 5.08 %RANDOM
Rwork0.1379 ---
all0.1391 62856 --
obs0.1391 62856 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.32 Å2 / Biso mean: 15.9161 Å2 / Biso min: 6.8 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 8 479 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023057
X-RAY DIFFRACTIONf_angle_d1.6744183
X-RAY DIFFRACTIONf_chiral_restr0.117447
X-RAY DIFFRACTIONf_plane_restr0.01554
X-RAY DIFFRACTIONf_dihedral_angle_d13.4771116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.62390.24581580.225532711
1.6239-1.64920.1841290.18625542683
1.6492-1.67630.2171250.171425682693
1.6763-1.70520.18431390.165925732712
1.7052-1.73620.17411210.159425592680
1.7362-1.76960.1831360.157825682704
1.7696-1.80570.18131220.144626022724
1.8057-1.84490.17141360.146825582694
1.8449-1.88780.16521510.146325612712
1.8878-1.9350.21711370.164525632700
1.935-1.98730.15941620.141525632725
1.9873-2.04580.18041500.128925442694
2.0458-2.11180.17421370.130125822719
2.1118-2.18720.17451230.129326112734
2.1872-2.27470.16851510.148725732724
2.2747-2.37820.14011270.134226172744
2.3782-2.50350.15571200.131325852705
2.5035-2.66020.1721600.132625872747
2.6602-2.86530.15641420.138226022744
2.8653-3.15320.13611470.129326402787
3.1532-3.60840.12611410.126226302771
3.6084-4.54220.15181350.118726692804
4.5422-25.69590.14481410.13628042945
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)
10.3642-0.1634-0.26870.82550.55121.05880.0081-0.1318-0.0702-0.01720.01290.0107-0.06160.0345-0.00470.1501-0.05870.02270.19650.02160.170933.419726.614612.7616
20.4611-0.17760.24121.17120.70621.0205-0.0731-0.0308-0.211-0.00440.02130.04910.1752-0.10150.03250.1456-0.04890.0360.09230.00690.151639.83119.78265.9686
30.5054-0.16050.02790.5787-0.17070.3446-0.00920.0751-0.1096-0.064-0.010.00350.1017-0.040.01880.1189-0.02280.01170.0885-0.00350.10844.670425.8074-3.1288
40.3995-0.0316-0.05110.21180.07760.4639-0.0003-0.0448-0.05520.0248-0.00110.01210.0835-0.0789-0.02690.13-0.0020.01150.11780.03850.1450.596227.546519.3418
50.3954-0.2537-0.29260.58650.00790.2999-0.0722-0.0953-0.19240.1380.02880.08580.0604-0.04730.04610.1525-0.0050.02380.17110.04080.120744.028735.742631.8084
60.627-0.21330.1940.8358-0.41041.18760.0049-0.1873-0.01970.18190.01370.0245-0.04910.0015-0.01540.1384-0.01570.00880.14040.01290.084545.987343.940630.2092
70.46460.02420.14730.46930.06630.70630.01440.00750.02920.04810.0035-0.0249-0.02350.0361-0.01170.0914-0.01120.01070.08820.00660.086348.965849.034818.3873
80.28780.0210.04960.23380.12650.2084-0.003-0.0181-0.04310.0177-0.0005-0.00450.04990.00170.00330.0986-0.00340.00870.08840.01210.100955.6434.295410.4919
91.05430.27840.40470.07730.08190.31850.0553-0.2455-0.06660.1206-0.0897-0.01510.2272-0.15660.02680.1642-0.02410.02230.14150.03350.171244.923721.633523.0089
102.06140.2383-0.52151.02030.25710.68180.00880.0429-0.3615-0.0421-0.01730.13440.1919-0.20620.0050.1936-0.06050.0220.14490.04250.190438.562215.56112.2976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:27)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28:51)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 52:113)A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 114:143)A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 144:170)A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 171:200)A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 201:249)A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 250:327)A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 328:354)A0
10X-RAY DIFFRACTION10CHAIN A AND (RESID 355:378)A0

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