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- PDB-4tv5: Crystal Structure of Citrate Synthase SbnG -

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Basic information

Entry
Database: PDB / ID: 4tv5
TitleCrystal Structure of Citrate Synthase SbnG
Components2-dehydro-3-deoxyglucarate aldolase
KeywordsLYASE / siderophore biosynthesis / iron / citrate synthase
Function / homology
Function and homology information


aldehyde-lyase activity / catalytic activity / metal ion binding / cytoplasm
Similarity search - Function
: / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxyglucarate aldolase / 2-dehydro-3-deoxyglucarate aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsKobylarz, M.J. / Grigg, J.C. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: SbnG, a Citrate Synthase in Staphylococcus aureus: A NEW FOLD ON AN OLD ENZYME.
Authors: Kobylarz, M.J. / Grigg, J.C. / Sheldon, J.R. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionJun 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 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 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydro-3-deoxyglucarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8353
Polymers28,7551
Non-polymers802
Water2,432135
1
A: 2-dehydro-3-deoxyglucarate aldolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)173,01018
Polymers172,5296
Non-polymers48112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation4_665-y+1,-x+1,-z1
crystal symmetry operation5_655-x+y+1,y,-z1
crystal symmetry operation6_555x,x-y,-z1
Buried area24350 Å2
ΔGint-284 kcal/mol
Surface area52650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.290, 74.290, 76.720
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operation: x,x-y,-z, -x+y+1,-x+1,z, -y+1,-x+1,-z, -y+1,x-y,z and -x+y+1,y,-z

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Components

#1: Protein 2-dehydro-3-deoxyglucarate aldolase


Mass: 28754.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: sbnG, NWMN_0066 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QDA6, UniProt: A0A0H3K9Z0*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.2 M calcium acetate, 0.1 M Imidazole, 4% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→76.72 Å / Num. all: 20780 / Num. obs: 20780 / % possible obs: 99.5 % / Redundancy: 8.6 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.095 / Rsym value: 0.089 / Net I/av σ(I): 4.957 / Net I/σ(I): 14.3 / Num. measured all: 178057
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.85-1.958.70.3142.42653030370.1120.3145.6100
1.95-2.078.80.2273.32495428510.0810.2277.3100
2.07-2.218.70.1634.52349326910.0580.1639.9100
2.21-2.398.60.1285.52164425110.0460.12813.2100
2.39-2.628.60.1036.61982723070.0370.10315.2100
2.62-2.938.60.0927.11803821040.0330.09218.1100
2.93-3.388.10.096.81512818570.0330.0921.299.9
3.38-4.147.60.0837.31174415380.0310.08323.896.9
4.14-5.859.20.0649.61133212310.0220.06427.4100
5.85-33.4338.20.0629.853676530.0240.06225.192.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å33.43 Å
Translation1.95 Å33.43 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.23phasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→76.72 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2189 / WRfactor Rwork: 0.1936 / FOM work R set: 0.8519 / SU B: 6.916 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1534 / SU Rfree: 0.1296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1062 5.1 %RANDOM
Rwork0.1967 19684 --
obs0.1975 20746 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.98 Å2 / Biso mean: 14.73 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 1.85→76.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 2 135 2046
Biso mean--37.1 20.28 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212076
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.9462836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4655273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3325100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21515365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9481513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211604
X-RAY DIFFRACTIONr_mcbond_it0.421.51306
X-RAY DIFFRACTIONr_mcangle_it0.76222134
X-RAY DIFFRACTIONr_scbond_it1.4183770
X-RAY DIFFRACTIONr_scangle_it2.3654.5702
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 73 -
Rwork0.313 1463 -
all-1536 -
obs--99.87 %
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)
112.67410.0417-0.50014.68356.18328.24190.11670.74511.3979-0.5408-0.29210.2968-0.8668-0.44090.17530.60830.16960.23320.21330.19710.55676.805830.161614.1938
20.85560.2256-0.22560.9142-0.10441.31270.0122-0.00960.0614-0.00560.0334-0.0557-0.0177-0.149-0.04560.05330.0008-0.00240.07790.00890.109722.290222.49339.3388
32.32090.7218-0.52984.1398-1.16652.18540.149-0.21860.05820.3704-0.1068-0.1041-0.0432-0.034-0.04220.1002-0.0215-0.00940.0815-0.01120.086722.668323.76227.2392
46.9635-0.4316-1.076210.80070.78284.40690.0292-0.0430.11030.0196-0.08540.0593-0.0438-0.00740.05620.06150.004-0.00230.0712-0.0280.081625.121737.528324.1573
51.78260.62910.12293.8144-1.57550.93450.0113-0.02440.06890.3196-0.07360.1176-0.107-0.08790.06240.156-0.01220.00150.118-0.0290.085417.144620.379325.6245
63.6379-1.3997-0.96316.40020.20074.0716-0.0052-0.2754-0.1470.34510.17850.3238-0.1674-0.0907-0.17340.0465-0.03150.02480.12440.01260.07468.087114.959829.5923
75.3961-0.7144-1.78833.2641-0.68236.49290.04960.1081-0.21320.04560.09610.3990.4045-0.304-0.14570.0595-0.0583-0.00080.1230.01030.11684.813713.168317.397
81.22471.23051.17929.74986.56658.55260.0265-0.1789-0.22340.3267-0.17560.31390.6319-0.62730.14910.1468-0.12440.03520.15070.04590.166314.0579-0.7068-2.0378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 16
2X-RAY DIFFRACTION2A17 - 89
3X-RAY DIFFRACTION3A90 - 107
4X-RAY DIFFRACTION4A108 - 121
5X-RAY DIFFRACTION5A132 - 189
6X-RAY DIFFRACTION6A190 - 212
7X-RAY DIFFRACTION7A213 - 236
8X-RAY DIFFRACTION8A237 - 258

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