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- PDB-4mmw: Crystal structure of D-glucarate dehydratase from Agrobacterium t... -

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Basic information

Entry
Database: PDB / ID: 4mmw
TitleCrystal structure of D-glucarate dehydratase from Agrobacterium tumefaciens complexed with magnesium, L-Xylarohydroxamate and L-Lyxarohydroxamate
ComponentsIsomerase/lactonizing enzyme
KeywordsISOMERASE / enolase fold / D-GLUCARATE DEHYDRATASE / L-Xylarohydroxamate / L-Lyxarohydroxamate
Function / homology
Function and homology information


hydro-lyase activity / isomerase activity / metal 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 / TRIETHYLENE GLYCOL / XYLAROHYDROXAMATE / Isomerase/lactonizing enzyme
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.647 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, L-Xylarohydroxamate and L-Lyxarohydroxamate
Authors: Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Gerlt, J.A. / Almo, S.C.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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)92,41223
Polymers90,9832
Non-polymers1,42921
Water13,349741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-130 kcal/mol
Surface area26950 Å2
MethodPISA
2
A: Isomerase/lactonizing enzyme
hetero molecules

B: Isomerase/lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,41223
Polymers90,9832
Non-polymers1,42921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
Buried area6790 Å2
ΔGint-136 kcal/mol
Surface area27460 Å2
MethodPISA
3
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)369,64892
Polymers363,9328
Non-polymers5,71684
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 area49240 Å2
ΔGint-531 kcal/mol
Surface area87750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.099, 118.099, 133.278
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: 45491.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu3453 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CSI0

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Non-polymers , 6 types, 762 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-XYH / XYLAROHYDROXAMATE


Mass: 194.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8NO7
#4: 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
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3.0M sodium chloride, 0.1M hepes, 5% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.647→49.101 Å / Num. all: 109435 / Num. obs: 109435 / % possible obs: 99.55 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata 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: 1.647→49.101 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 5470 5 %RANDOM
Rwork0.1702 ---
all0.1714 109435 --
obs0.1714 109435 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.647→49.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6018 0 78 741 6837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066323
X-RAY DIFFRACTIONf_angle_d1.0698586
X-RAY DIFFRACTIONf_dihedral_angle_d12.2082367
X-RAY DIFFRACTIONf_chiral_restr0.07913
X-RAY DIFFRACTIONf_plane_restr0.0051126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6472-1.66590.28851600.28143446X-RAY DIFFRACTION98
1.6659-1.68550.32351560.26893445X-RAY DIFFRACTION100
1.6855-1.7060.26661700.2553491X-RAY DIFFRACTION100
1.706-1.72760.28561910.24273459X-RAY DIFFRACTION100
1.7276-1.75040.29342040.24633435X-RAY DIFFRACTION100
1.7504-1.77440.27411880.24243471X-RAY DIFFRACTION100
1.7744-1.79970.28241830.22153475X-RAY DIFFRACTION100
1.7997-1.82660.25361760.22093438X-RAY DIFFRACTION100
1.8266-1.85510.24051770.2123507X-RAY DIFFRACTION100
1.8551-1.88550.22611770.20743475X-RAY DIFFRACTION100
1.8855-1.9180.2371790.19553471X-RAY DIFFRACTION100
1.918-1.95290.24632000.19743444X-RAY DIFFRACTION100
1.9529-1.99050.24311920.19513428X-RAY DIFFRACTION100
1.9905-2.03110.23111850.1843490X-RAY DIFFRACTION100
2.0311-2.07530.20011740.18213483X-RAY DIFFRACTION100
2.0753-2.12360.22432100.17943425X-RAY DIFFRACTION100
2.1236-2.17670.21661980.17933478X-RAY DIFFRACTION100
2.1767-2.23550.20291960.17623429X-RAY DIFFRACTION100
2.2355-2.30130.22411920.17283446X-RAY DIFFRACTION99
2.3013-2.37560.21382180.18853431X-RAY DIFFRACTION99
2.3756-2.46050.21651590.17953452X-RAY DIFFRACTION99
2.4605-2.5590.20841620.17873464X-RAY DIFFRACTION99
2.559-2.67540.2171890.19053473X-RAY DIFFRACTION99
2.6754-2.81650.20931590.18823467X-RAY DIFFRACTION99
2.8165-2.99290.20581610.19333462X-RAY DIFFRACTION99
2.9929-3.2240.18981710.17313492X-RAY DIFFRACTION99
3.224-3.54830.16031790.14283492X-RAY DIFFRACTION100
3.5483-4.06160.13371710.1183498X-RAY DIFFRACTION100
4.0616-5.11630.13191970.11663471X-RAY DIFFRACTION100
5.1163-49.12250.15271960.14893527X-RAY DIFFRACTION99
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)
10.42340.03760.05250.3646-0.04670.6236-0.0103-0.04290.06650.0446-0.0112-0.0249-0.11730.05320.0210.1653-0.0193-0.00770.1338-0.01110.152914.054829.704812.8232
20.38760.05330.05660.425-0.04520.6303-0.00790.04290.0312-0.0442-0.0125-0.0747-0.05930.11810.01970.1219-0.02070.01340.15320.00680.142329.746314.0792-13.2144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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