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- PDB-4hch: CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM T... -

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Basic information

Entry
Database: PDB / ID: 4hch
TitleCRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed with magnesium and L-tartrate
ComponentsIsomerase/lactonizing enzyme
KeywordsISOMERASE / Enolase fold / D-GLUCARATE DEHYDRATASE / D-GLUCARATE
Function / homology
Function and homology information


hydro-lyase activity / carbohydrate catabolic process / isomerase activity / magnesium ion binding
Similarity search - Function
: / 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 ...: / 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
TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / Isomerase/lactonizing enzyme
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Sakai, A. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed with magnesium and L-tartrate
Authors: Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Gerlt, J.A. / Almo, S.C.
History
DepositionSep 29, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 24, 2012ID: 3SHH
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_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: Isomerase/lactonizing enzyme
B: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,75422
Polymers90,2682
Non-polymers1,48620
Water17,114950
1
A: Isomerase/lactonizing enzyme
hetero molecules

B: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,75422
Polymers90,2682
Non-polymers1,48620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
Buried area2990 Å2
ΔGint-8 kcal/mol
Surface area28050 Å2
MethodPISA
2
A: Isomerase/lactonizing enzyme
B: Isomerase/lactonizing enzyme
hetero molecules

A: Isomerase/lactonizing enzyme
B: Isomerase/lactonizing enzyme
hetero molecules

A: Isomerase/lactonizing enzyme
B: Isomerase/lactonizing enzyme
hetero molecules

A: Isomerase/lactonizing enzyme
B: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,01888
Polymers361,0728
Non-polymers5,94680
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area31630 Å2
ΔGint-52 kcal/mol
Surface area92530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.252, 118.252, 133.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Isomerase/lactonizing enzyme


Mass: 45133.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu3453 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CSI0

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Non-polymers , 7 types, 970 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 950 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 0.2M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, pH 7.0, 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: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.699→37.793 Å / Num. all: 98528 / Num. obs: 98528 / % possible obs: 98.27 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RVK

1rvk


Resolution: 1.699→37.793 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 16.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.171 4917 4.99 %RANDOM
Rwork0.141 ---
all0.1425 98528 --
obs0.1425 98528 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→37.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 94 950 7118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066370
X-RAY DIFFRACTIONf_angle_d1.0848632
X-RAY DIFFRACTIONf_dihedral_angle_d12.6712344
X-RAY DIFFRACTIONf_chiral_restr0.07912
X-RAY DIFFRACTIONf_plane_restr0.0051126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6989-1.71830.25551330.22772551X-RAY DIFFRACTION80
1.7183-1.73850.2941380.22542756X-RAY DIFFRACTION88
1.7385-1.75970.26271470.22382908X-RAY DIFFRACTION92
1.7597-1.78190.25251560.21963054X-RAY DIFFRACTION95
1.7819-1.80540.24111690.19473043X-RAY DIFFRACTION97
1.8054-1.83010.20651730.18273067X-RAY DIFFRACTION98
1.8301-1.85630.20481500.16993190X-RAY DIFFRACTION99
1.8563-1.8840.21941720.16343154X-RAY DIFFRACTION100
1.884-1.91340.2021540.16073202X-RAY DIFFRACTION100
1.9134-1.94480.19361610.1543183X-RAY DIFFRACTION100
1.9448-1.97830.18671740.15573140X-RAY DIFFRACTION100
1.9783-2.01430.17761660.14643163X-RAY DIFFRACTION100
2.0143-2.0530.20171720.14023154X-RAY DIFFRACTION100
2.053-2.09490.15961710.13863171X-RAY DIFFRACTION100
2.0949-2.14050.16311600.13463190X-RAY DIFFRACTION100
2.1405-2.19030.1851800.13553142X-RAY DIFFRACTION100
2.1903-2.2450.15671540.13383145X-RAY DIFFRACTION100
2.245-2.30570.16861910.13553166X-RAY DIFFRACTION100
2.3057-2.37360.1891510.14153230X-RAY DIFFRACTION100
2.3736-2.45020.16641500.13793177X-RAY DIFFRACTION100
2.4502-2.53770.18961560.1443185X-RAY DIFFRACTION100
2.5377-2.63930.17871630.14923149X-RAY DIFFRACTION100
2.6393-2.75940.15611770.1353188X-RAY DIFFRACTION100
2.7594-2.90480.15681710.13733179X-RAY DIFFRACTION100
2.9048-3.08670.16671810.13323148X-RAY DIFFRACTION100
3.0867-3.32490.16031850.13393178X-RAY DIFFRACTION100
3.3249-3.65930.14841580.12613186X-RAY DIFFRACTION100
3.6593-4.18820.12661600.11083190X-RAY DIFFRACTION100
4.1882-5.27440.13571620.11153213X-RAY DIFFRACTION100
5.2744-37.80220.16451820.14573209X-RAY DIFFRACTION99

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