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- PDB-6u7l: 2.75 Angstrom Crystal Structure of Galactarate Dehydratase from E... -

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Basic information

Entry
Database: PDB / ID: 6u7l
Title2.75 Angstrom Crystal Structure of Galactarate Dehydratase from Escherichia coli.
Components(Galactarate dehydratase (L-threo-forming)) x 2
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / galactarate dehydratase / garD
Function / homology
Function and homology information


galactarate dehydratase / D-galacturonate catabolic process / galactarate catabolic process / galactarate dehydratase activity / ferrous iron binding / protein homodimerization activity
Similarity search - Function
Galactarate dehydratase GarD-like / Galactarate dehydratase (L-threo-forming) GarD, Enterobacteriaceae / UxaA/GarD, SAF domain / : / D-galactarate/Altronate dehydratase, C-terminal / D-galactarate/Altronate dehydratase, C-terminal / D-galactarate dehydratase/Altronate hydrolase, second domain / SAF domain / SAF domain / SAF
Similarity search - Domain/homology
Galactarate dehydratase (L-threo-forming)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsMinasov, G. / Shuvalova, L. / Wawrzak, Z. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Protein Sci. / Year: 2020
Title: Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment.
Authors: Rosas-Lemus, M. / Minasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Mih, N. / Jaroszewski, L. / Palsson, B. / Godzik, A. / Satchell, K.J.F.
History
DepositionSep 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactarate dehydratase (L-threo-forming)
B: Galactarate dehydratase (L-threo-forming)
C: Galactarate dehydratase (L-threo-forming)
D: Galactarate dehydratase (L-threo-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,75520
Polymers229,1464
Non-polymers60916
Water2,702150
1
A: Galactarate dehydratase (L-threo-forming)
B: Galactarate dehydratase (L-threo-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,99511
Polymers114,6532
Non-polymers3429
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-97 kcal/mol
Surface area37640 Å2
MethodPISA
2
C: Galactarate dehydratase (L-threo-forming)
D: Galactarate dehydratase (L-threo-forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7609
Polymers114,4932
Non-polymers2677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-80 kcal/mol
Surface area37360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.462, 167.574, 117.065
Angle α, β, γ (deg.)90.000, 103.970, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A14 - 523
2010B14 - 523
1020A10 - 523
2020C10 - 523
1030A12 - 523
2030D12 - 523
1040B14 - 522
2040C14 - 522
1050B14 - 523
2050D14 - 523
1060C12 - 523
2060D12 - 523

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Galactarate dehydratase (L-threo-forming) / GalcD


Mass: 57326.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: garD, yhaG, b3128, JW3097 / Variant: MG1655 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Magic / References: UniProt: P39829, galactarate dehydratase
#2: Protein Galactarate dehydratase (L-threo-forming) / GalcD


Mass: 57246.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: garD, yhaG, b3128, JW3097 / Variant: MG1655 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Magic / References: UniProt: P39829, galactarate dehydratase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein: 7.6 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3; Screen: PACT (D11), 0.2M Calcium chloride, 0.1M Tris pH 8.0, 20% (w/v) PEG 6000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 56199 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 59.2 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.044 / Rrim(I) all: 0.109 / Rsym value: 0.1 / Χ2: 1.115 / Net I/σ(I): 16.7
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2851 / CC1/2: 0.779 / Rpim(I) all: 0.349 / Rrim(I) all: 0.867 / Rsym value: 0.793 / Χ2: 1.001 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→29.23 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 29.778 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.347
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 2734 4.9 %RANDOM
Rwork0.2065 ---
obs0.2082 53337 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 222.69 Å2 / Biso mean: 72.094 Å2 / Biso min: 27.52 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å2-1.47 Å2
2---7.34 Å20 Å2
3---4.06 Å2
Refinement stepCycle: final / Resolution: 2.75→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13852 0 16 150 14018
Biso mean--82.58 56.02 -
Num. residues----1816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314197
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713356
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.64519292
X-RAY DIFFRACTIONr_angle_other_deg0.3211.56830959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.74551804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.80622.764662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.565152175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.641576
X-RAY DIFFRACTIONr_chiral_restr0.0530.21886
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.0215860
X-RAY DIFFRACTIONr_gen_planes_other0.0490.022776
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A134240.09
12B134240.09
21A136890.08
22C136890.08
31A134340.09
32D134340.09
41B133520.09
42C133520.09
51B133480.09
52D133480.09
61C133520.1
62D133520.1
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 210 -
Rwork0.301 3849 -
all-4059 -
obs--97.29 %
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)
14.6965-3.4984-0.62624.1892-0.67881.8518-0.0522-0.06910.2736-0.13970.1651-0.0697-0.4638-0.2104-0.11290.40090.0352-0.06130.29530.17040.1709-9.131742.0509231.6366
22.92832.64580.65925.21430.34782.2408-0.00320.2658-0.1328-0.35380.0194-0.17560.18320.0994-0.01610.07030.05810.04220.29470.03340.08722.2947-1.2777241.3407
31.7862.4931.31995.27341.44481.13020.12960.4834-0.328-0.7485-0.069-0.690.42680.5038-0.06060.79340.23970.29590.7130.04840.4033.0665-4.3203229.7881
40.65510.10240.41751.34120.14741.7647-0.01880.28630.0753-0.5457-0.0798-0.3282-0.18050.18060.09870.23860.00910.12740.41810.09180.10162.728912.775233.6013
50.6822-0.0269-0.0621.3397-0.50520.7879-0.07330.1240.0924-0.3006-0.0371-0.0906-0.0853-0.00640.11040.15730.0145-0.0080.3560.09340.0574-2.405317.4379239.122
66.9878-3.1304-2.72269.8774-2.16522.4236-0.26440.0812-0.754-1.2971-0.2147-0.16670.59740.08520.47910.9076-0.12430.13910.3077-0.02360.1138-8.6856-30.2949199.2402
71.69511.1637-1.91272.53480.58844.4884-0.52250.23260.2183-1.08750.09540.79830.042-0.39290.4270.70940.0077-0.36990.50980.06930.286-27.9133-13.6674208.3104
81.91191.3167-0.82212.97051.22996.1065-0.096-0.28820.2093-0.577-0.10550.5945-0.289-0.13580.20150.1522-0.0163-0.07750.3068-0.08260.2707-25.01861.1695235.8321
90.78270.66180.51863.13821.23892.1037-0.15920.11510.0508-0.87380.0120.4962-0.0687-0.27480.14710.2938-0.0811-0.14570.330.00470.0836-24.1088-9.8375220.7138
102.12981.12440.34652.37321.3152.198-0.1113-0.22640.0561-0.3737-0.24990.58420.4297-0.37460.36120.3726-0.0666-0.09390.4838-0.04930.1778-23.4769-17.7558225.412
114.45383.2012.23443.34270.58152.78530.3116-0.2461-0.47470.45640.11960.03440.2653-0.2635-0.43120.25570.09140.14540.240.16140.23645.8296-23.9358281.7289
122.3256-1.6875-0.71584.78980.96852.1722-0.0504-0.11990.30710.07520.0331-0.0216-0.14340.07120.01730.0442-0.03820.05140.3780.01060.232418.558217.8407270.0833
131.60040.2702-0.36582.52790.3221.270.0522-0.14020.24660.49690.0643-0.40310.0860.1489-0.11650.14610.0052-0.0120.50830.02030.221519.275414.4473272.579
146.7653-3.13370.22443.59040.45784.6387-0.0118-0.416-0.11160.6722-0.1440.02940.14950.19420.15570.2765-0.01450.02240.25680.07120.02418.9069-3.8715291.3016
151.196-0.03520.50921.94220.08851.9335-0.046-0.03680.05970.3798-0.01030.03690.15410.12740.05630.12530.01940.07410.41730.04550.127413.6526-0.157272.8949
165.48447.35680.414611.1148-1.42967.08290.1342-0.23840.64321.0472-0.3489-0.0513-0.83811.05670.21470.73830.0398-0.51890.6168-0.46241.3126.989252.8842305.3567
173.77340.78130.15023.8162-2.78662.2592-0.1363-1.61970.15041.6553-0.7413-1.073-1.02210.38570.87761.9320.0645-0.50331.476-0.39161.04643.565638.685315.0622
181.1796-1.1465-0.56982.89732.18893.3925-0.1369-0.0233-0.24250.3438-0.04860.59310.38-0.03910.18550.0729-0.01330.09910.2512-0.01030.2637-12.344319.2044277.404
190.6203-0.6649-0.00752.58690.89130.7149-0.2071-0.15180.14750.79060.04660.17040.2154-0.120.16050.27760.04050.09160.3666-0.07670.1678-10.575126.4745291.8065
201.2785-0.9542-0.61971.39361.32641.5007-0.0476-0.11290.2990.0540.1122-0.1841-0.04520.0514-0.06460.1143-0.00150.05080.2833-0.09930.2613-4.07837.6225284.7068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 110
2X-RAY DIFFRACTION2A111 - 176
3X-RAY DIFFRACTION3A186 - 248
4X-RAY DIFFRACTION4A249 - 377
5X-RAY DIFFRACTION5A378 - 523
6X-RAY DIFFRACTION6B14 - 85
7X-RAY DIFFRACTION7B86 - 130
8X-RAY DIFFRACTION8B131 - 208
9X-RAY DIFFRACTION9B209 - 476
10X-RAY DIFFRACTION10B477 - 523
11X-RAY DIFFRACTION11C9 - 109
12X-RAY DIFFRACTION12C110 - 187
13X-RAY DIFFRACTION13C188 - 319
14X-RAY DIFFRACTION14C320 - 377
15X-RAY DIFFRACTION15C378 - 523
16X-RAY DIFFRACTION16D12 - 54
17X-RAY DIFFRACTION17D55 - 107
18X-RAY DIFFRACTION18D108 - 249
19X-RAY DIFFRACTION19D250 - 434
20X-RAY DIFFRACTION20D435 - 523

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