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- PDB-4hyr: Structure of putative Glucarate dehydratase from Acidaminococcus ... -

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Basic information

Entry
Database: PDB / ID: 4hyr
TitleStructure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder
ComponentsGlucarate dehydratase
KeywordsLYASE / Glucarate dehydratase / New York Structural Genomics Research Consortium / NYSGRC / Protein Structure Initiative / PSI-Biology
Function / homology
Function and homology information


D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / 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 ...D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / 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
Putative glucarate dehydratase
Similarity search - Component
Biological speciesAcidaminococcus sp. D21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.84 Å
AuthorsHegde, R.P. / Toro, R. / Burley, S.K. / Almo, S.C. / Ramagopal, U.A. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be published
Title: Structure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder
Authors: Hegde, R.P. / Toro, R. / Burley, S.K. / Almo, S.C. / Ramagopal, U.A. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Glucarate dehydratase
B: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04410
Polymers102,5682
Non-polymers4778
Water9,512528
1
A: Glucarate dehydratase
B: Glucarate dehydratase
hetero molecules

A: Glucarate dehydratase
B: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,08920
Polymers205,1354
Non-polymers95416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-30 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.916, 88.916, 236.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

21B-715-

HOH

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Components

#1: Protein Glucarate dehydratase


Mass: 51283.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus sp. D21 (bacteria) / Gene: ACDG_00756 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0WBB5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 82827 / Num. obs: 82827 / % possible obs: 99.5 % / Redundancy: 23.8 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.079 / Χ2: 1.378 / Net I/σ(I): 37.238
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.84-1.8722.40.973.87537000.8951.21990.2
1.87-1.9124.40.81340831.218100
1.91-1.9424.50.71541111.237100
1.94-1.9824.50.59140681.242100
1.98-2.0324.50.49240981.272100
2.03-2.0724.40.40841231.253100
2.07-2.1224.50.33640761.274100
2.12-2.1824.40.28541131.326100
2.18-2.2524.40.24841081.336100
2.25-2.3224.40.22141181.384100
2.32-2.424.40.1941401.334100
2.4-2.524.30.1741121.377100
2.5-2.6124.30.14241551.409100
2.61-2.7524.20.12441481.4100
2.75-2.9224.10.10841711.463100
2.92-3.1523.80.09241981.413100
3.15-3.4623.30.08241911.342100
3.46-3.9622.60.0742411.377100
3.96-4.9921.70.05843021.649100
4.99-5020.40.05945712.08799.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
ARP/wARPmodel building
HKL2Mapphasing
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.84→43.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1964 / WRfactor Rwork: 0.1583 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8879 / SU B: 4.97 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1276 / SU Rfree: 0.1201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 4129 5 %RANDOM
Rwork0.1629 ---
obs0.1647 82357 99.47 %-
all-82357 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.73 Å2 / Biso mean: 26.0755 Å2 / Biso min: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6824 0 27 528 7379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197695
X-RAY DIFFRACTIONr_bond_other_d00.027263
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.97110462
X-RAY DIFFRACTIONr_angle_other_deg0.695316773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3623.923362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.359151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4551555
X-RAY DIFFRACTIONr_chiral_restr0.0850.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218873
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021768
LS refinement shellResolution: 1.842→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 275 -
Rwork0.226 5625 -
all-5900 -
obs--98.32 %
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)
10.4105-0.10530.3890.4391-0.39040.75680.06970.0312-0.005-0.0562-0.020.06820.1340.0384-0.04970.18570.0089-0.03110.1923-0.02040.1214-0.159337.878857.535
20.40970.0310.18130.1973-0.06730.2225-0.0727-0.030.1259-0.01270.01380.00350.0054-0.04520.0590.15260.0141-0.03250.1739-0.01350.1781-1.760356.959655.8437
30.9428-0.08870.05680.3765-0.21190.2301-0.0755-0.14290.03820.1887-0.0007-0.0406-0.1307-0.10.07620.21270.0058-0.04920.2221-0.04060.076617.490846.257192.9418
40.1790.0999-0.00590.3884-0.14280.16710.0198-0.0306-0.00450.0363-0.073-0.15440.0107-0.02280.05320.16370.0057-0.03940.18120.02380.188133.495442.25480.5846
50.34960.13191.42350.9736-1.970712.60620.082-0.1943-0.25370.6779-0.2136-0.5293-1.359-0.44450.13150.4721-0.1414-0.370.12570.2010.387644.636455.077693.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2A104 - 442
3X-RAY DIFFRACTION3B1 - 89
4X-RAY DIFFRACTION4B101 - 412
5X-RAY DIFFRACTION5B413 - 442

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