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

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Basic information

Entry
Database: PDB / ID: 4hcl
TitleCRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed with magnesium and L-Lyxarohydroxamate
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
Chem-LLH / Isomerase/lactonizing enzyme
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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-Lyxarohydroxamate
Authors: Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Gerlt, J.A. / Almo, S.C.
History
DepositionSep 30, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 24, 2012ID: 3TU2
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_seq_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.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)90,9509
Polymers90,2682
Non-polymers6827
Water10,665592
1
A: Isomerase/lactonizing enzyme
hetero molecules

B: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9509
Polymers90,2682
Non-polymers6827
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
Buried area3000 Å2
ΔGint-8 kcal/mol
Surface area28110 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)363,79936
Polymers361,0728
Non-polymers2,72728
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 area32090 Å2
ΔGint-38 kcal/mol
Surface area92370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.260, 118.260, 133.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-LLH / (2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID


Mass: 195.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO7
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 52.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.0 M SODIUM CHLORIDE, 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: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 28, 2011
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: 1.8→37.397 Å / Num. all: 80784 / Num. obs: 80784 / % possible obs: 95.51 % / 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: 1.8→37.397 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 4056 5.02 %RANDOM
Rwork0.1839 ---
all0.1856 80784 --
obs0.1856 80784 95.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→37.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 43 592 6709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076320
X-RAY DIFFRACTIONf_angle_d1.0898576
X-RAY DIFFRACTIONf_dihedral_angle_d12.9522341
X-RAY DIFFRACTIONf_chiral_restr0.073909
X-RAY DIFFRACTIONf_plane_restr0.0051123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82120.304870.25311674X-RAY DIFFRACTION60
1.8212-1.84340.2886990.2482015X-RAY DIFFRACTION73
1.8434-1.86670.33831010.24562257X-RAY DIFFRACTION82
1.8667-1.89130.27251260.2482458X-RAY DIFFRACTION90
1.8913-1.91720.27381250.23582629X-RAY DIFFRACTION93
1.9172-1.94460.27111330.24542702X-RAY DIFFRACTION96
1.9446-1.97360.26951490.22382677X-RAY DIFFRACTION98
1.9736-2.00450.27191580.23432757X-RAY DIFFRACTION99
2.0045-2.03730.28391520.22982681X-RAY DIFFRACTION100
2.0373-2.07240.24321400.21932790X-RAY DIFFRACTION100
2.0724-2.11010.271450.21282768X-RAY DIFFRACTION100
2.1101-2.15070.23731340.20882779X-RAY DIFFRACTION100
2.1507-2.19460.27341690.20972715X-RAY DIFFRACTION100
2.1946-2.24230.23711550.20322752X-RAY DIFFRACTION100
2.2423-2.29450.25261480.19622739X-RAY DIFFRACTION99
2.2945-2.35180.29681530.22622741X-RAY DIFFRACTION99
2.3518-2.41540.25681350.21252762X-RAY DIFFRACTION99
2.4154-2.48650.28551480.2232729X-RAY DIFFRACTION99
2.4865-2.56670.25561440.21112725X-RAY DIFFRACTION98
2.5667-2.65840.30131480.21812702X-RAY DIFFRACTION98
2.6584-2.76480.25311620.21212680X-RAY DIFFRACTION98
2.7648-2.89060.22031120.20542764X-RAY DIFFRACTION98
2.8906-3.0430.2071370.20142702X-RAY DIFFRACTION98
3.043-3.23350.2341520.19312744X-RAY DIFFRACTION99
3.2335-3.4830.18221470.1612770X-RAY DIFFRACTION99
3.483-3.83320.17571600.14582717X-RAY DIFFRACTION98
3.8332-4.38710.13621570.12732702X-RAY DIFFRACTION98
4.3871-5.52450.15321280.13462791X-RAY DIFFRACTION99
5.5245-37.40520.17911520.15812806X-RAY DIFFRACTION99

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