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- PDB-5x8g: Binary complex structure of a double mutant I454RA456K of o-Succi... -

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Basic information

Entry
Database: PDB / ID: 5x8g
TitleBinary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with its product analogue OSB-NCoA at 1.90 angstrom
Components2-succinylbenzoate--CoA ligase
KeywordsLIGASE / Adenylate-forming Enzyme / acyl-CoA synthetase / thioester conformation / CoA / pantetheine tunnel / ADP binding subsite / domain alternation / large conformational change / inter-domain linker
Function / homology
Function and homology information


o-succinylbenzoate-CoA ligase / o-succinylbenzoate-CoA ligase activity / CoA-ligase activity / menaquinone biosynthetic process / ATP binding
Similarity search - Function
2-succinylbenzoate--CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase ...2-succinylbenzoate--CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / o-succinylbenzoyl-N-coenzyme A / 2-succinylbenzoate--CoA ligase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, Y. / Guo, Z.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode
Authors: Chen, Y. / Li, T.L. / Lin, X. / Li, X. / Li, X.D. / Guo, Z.
History
DepositionMar 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop ...pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3Nov 22, 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-succinylbenzoate--CoA ligase
B: 2-succinylbenzoate--CoA ligase
D: 2-succinylbenzoate--CoA ligase
C: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,10837
Polymers216,8924
Non-polymers5,21633
Water30,2471679
1
A: 2-succinylbenzoate--CoA ligase
C: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,26921
Polymers108,4462
Non-polymers2,82419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-101 kcal/mol
Surface area37120 Å2
MethodPISA
2
B: 2-succinylbenzoate--CoA ligase
D: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,83816
Polymers108,4462
Non-polymers2,39214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-82 kcal/mol
Surface area36790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.950, 96.480, 97.660
Angle α, β, γ (deg.)80.140, 77.810, 81.170
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABDC

#1: Protein
2-succinylbenzoate--CoA ligase / o-succinylbenzoyl-CoA synthetase / OSB-CoA synthetase


Mass: 54222.945 Da / Num. of mol.: 4 / Fragment: UNP residues 2-486 / Mutation: I454R, A456K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: menE, BSU30790 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P23971, o-succinylbenzoate-CoA ligase

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Non-polymers , 6 types, 1712 molecules

#2: Chemical
ChemComp-S0N / o-succinylbenzoyl-N-coenzyme A


Mass: 954.663 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H45N8O20P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1679 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Reservoir solution: 32%(v/v) PEG300, 0.15M sodium cacodylate (pH 6.5), 0.2M Calcium acetate. Protein solution: 2.5mM OSB-NCoA, 16mg/mL protein, 10mM MgCl2. Crystals appeared after 4 days incubation.
PH range: 6.2-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→31.03 Å / Num. obs: 181132 / % possible obs: 91.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 22.93 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.06 / Rrim(I) all: 0.139 / Net I/σ(I): 8.5 / Num. measured all: 892667 / Scaling rejects: 4119
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.8 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.930.8164412791320.8110.3980.9092.492.8
10.41-31.030.09535211040.980.0460.10116.391.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.2data extraction
Aimless0.5.26data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X8F

5x8f


Resolution: 1.9→31.027 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1988 1.1 %
Rwork0.1636 179058 -
obs0.1641 181046 91.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.64 Å2 / Biso mean: 31.8452 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: final / Resolution: 1.9→31.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14679 0 323 1679 16681
Biso mean--32.36 39.36 -
Num. residues----1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715442
X-RAY DIFFRACTIONf_angle_d0.86120998
X-RAY DIFFRACTIONf_chiral_restr0.0552390
X-RAY DIFFRACTIONf_plane_restr0.0052679
X-RAY DIFFRACTIONf_dihedral_angle_d15.3339232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94750.24631380.2342129711310993
1.9475-2.00020.25161490.2077129221307192
2.0002-2.0590.23991460.1917129111305792
2.059-2.12540.2441360.1807128711300792
2.1254-2.20140.20161440.171128891303392
2.2014-2.28950.21671400.1675128571299792
2.2895-2.39370.20841510.169128681301992
2.3937-2.51980.21221380.1675127841292292
2.5198-2.67760.24171470.1681128511299892
2.6776-2.88420.23271450.172128731301892
2.8842-3.17420.23411420.1716127441288691
3.1742-3.63290.20391400.1546126391277990
3.6329-4.57470.16621290.1316118791200885
4.5747-31.0310.17131430.1557129991314293
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)
11.81510.5567-0.51771.6292-1.13641.49620.0796-0.1279-0.15410.045-0.2261-0.20.08980.27070.12420.18430.041-0.00190.18360.01090.1308119.40423.209-89.8886
21.53640.2614-0.2641.2124-0.7382.31570.043-0.14530.01670.191-0.0539-0.0098-0.12210.09150.00430.1697-0.00070.01150.1226-0.03420.1123109.832513.0021-90.3392
31.31150.05570.0350.7585-0.81172.19780.01760.0014-0.0231-0.03920.14060.1820.172-0.4477-0.10390.1737-0.0349-0.00240.2232-0.02480.179291.34764.9268-96.838
42.2440.41840.06461.36550.6740.34620.0070.15380.4252-0.1905-0.31370.6064-0.193-0.61430.06680.24530.0208-0.08350.77540.0580.638775.0516-0.2449-86.2878
51.6107-0.12020.13691.1808-0.39541.09860.02780.31970.0591-0.2624-0.03560.06450.0324-0.0086-0.00210.16240.0092-0.01680.16410.02290.144595.835-26.576-118.847
61.1494-0.06220.12412.56730.30180.7874-0.076-0.05550.3050.2501-0.0058-0.2272-0.17430.15160.10010.2-0.0122-0.0420.16280.02030.2381109.936-32.077-137.244
73.0862-0.43691.45050.8942-0.98173.4668-0.00520.146-0.0943-0.0349-0.0801-0.1429-0.10710.28510.00680.14650.02430.03660.17460.04130.1964115.878-11.105-130.173
80.50410.2239-0.33381.03250.37470.70960.14910.4320.4607-0.2414-0.0828-0.4004-0.07460.0819-0.04960.2870.04360.1110.44130.18150.4472128.74-29.421-113.316
91.7539-0.49580.84021.1221-0.85891.85540.0754-0.0803-0.13040.09110.07960.11130.0691-0.1906-0.1450.1432-0.00440.02480.1222-0.00770.1475113.35229.702-128.189
101.8876-0.32380.82821.5476-0.62871.23350.1680.192-0.1403-0.1312-0.05780.00350.22070.14530.00220.1430.0312-0.00110.1431-0.05290.1229121.97833.528-117.876
112.26760.0821-0.87421.6034-1.54041.8427-0.04210.28550.3362-0.0484-0.16-0.2787-0.11730.33670.02730.1284-0.0327-0.00110.26490.06120.2554136.71319.273-112.033
122.7846-0.14110.51051.65870.09611.50250.10880.1686-0.04530.2449-0.0663-0.58750.00360.3905-0.02250.20660.0003-0.08740.2438-0.01480.3951148.22433.88-132.913
131.6689-0.36850.17161.5915-0.19061.1006-0.09410.18280.3638-0.1414-0.0146-0.0794-0.27720.08990.07970.2143-0.0625-0.01840.21050.08460.242795.54856.4179-149.5263
141.3092-0.01790.4210.9011-0.11561.6491-0.05930.13410.1328-0.09270.0223-0.0039-0.02860.0155-0.0070.1132-0.010.01650.17950.05910.136686.6751-6.3963-149.8896
152.49250.27590.65211.9706-1.4141.7372-0.1149-0.3113-0.01620.12370.28980.33440.0015-0.5202-0.00260.14850.04510.04730.39610.07440.230373.6769-9.3139-133.5707
162.4719-0.1810.66112.43980.63891.5725-0.23720.05220.6309-0.0316-0.02030.4547-0.4788-0.60560.05320.34880.1575-0.08260.50890.07910.502661.12998.4669-151.6363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:110)A2 - 110
2X-RAY DIFFRACTION2(chain A and resid 111:283)A111 - 283
3X-RAY DIFFRACTION3(chain A and resid 284:474)A284 - 474
4X-RAY DIFFRACTION4(chain A and resid 475:485)A475 - 485
5X-RAY DIFFRACTION5(chain B and resid 2:217)B2 - 217
6X-RAY DIFFRACTION6(chain B and resid 218:302)B218 - 302
7X-RAY DIFFRACTION7(chain B and resid 303:381)B303 - 381
8X-RAY DIFFRACTION8(chain B and resid 382:485)B382 - 485
9X-RAY DIFFRACTION9(chain C and resid 2:111)C2 - 111
10X-RAY DIFFRACTION10(chain C and resid 112:283)C112 - 283
11X-RAY DIFFRACTION11(chain C and resid 284:381)C284 - 381
12X-RAY DIFFRACTION12(chain C and resid 382:485)C382 - 485
13X-RAY DIFFRACTION13(chain D and resid 2:116)D2 - 116
14X-RAY DIFFRACTION14(chain D and resid 117:300)D117 - 300
15X-RAY DIFFRACTION15(chain D and resid 301:380)D301 - 380
16X-RAY DIFFRACTION16(chain D and resid 381:485)D381 - 485

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