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- PDB-5x8f: Ternary complex structure of a double mutant I454RA456K of o-Succ... -

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Basic information

Entry
Database: PDB / ID: 5x8f
TitleTernary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with AMP and its product analogue OSB-NCoA at 1.76 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, N-terminal domain / ANL, C-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. / AMP-dependent synthetase/ligase ...2-succinylbenzoate--CoA ligase / : / ANL, N-terminal domain / ANL, C-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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 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: 1.763 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 1.2Nov 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_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.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.ptnr2_symmetry / _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_ptnr1_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.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_label_seq_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
C: 2-succinylbenzoate--CoA ligase
D: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,68380
Polymers216,8924
Non-polymers6,79176
Water36,6062032
1
A: 2-succinylbenzoate--CoA ligase
C: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,14537
Polymers108,4462
Non-polymers3,69935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-11 kcal/mol
Surface area36710 Å2
MethodPISA
2
B: 2-succinylbenzoate--CoA ligase
D: 2-succinylbenzoate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,53843
Polymers108,4462
Non-polymers3,09241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-11 kcal/mol
Surface area36460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.870, 96.360, 98.070
Angle α, β, γ (deg.)80.440, 77.960, 81.110
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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 , 7 types, 2108 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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2032 / 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: 3 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: Reservoir solution: 32% PEG300, 0.1M cacodylate pH6.7, 0.2M Ca(OAc)2, protein solution: 2.5mM OSBNCoA, 0.8mM AMP, 19mg/mL bsMenE I454RA456K, incubated for 4days
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: 1.76→36.99 Å / Num. obs: 230857 / % possible obs: 92.1 % / Redundancy: 2 % / Biso Wilson estimate: 21.19 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.047 / Rrim(I) all: 0.066 / Rsym value: 0.082 / Net I/av σ(I): 10.5 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
1.76-1.793.90.3721.9112180.8270.3720.5250.60690.8
9.66-36.991.80.0290.9920.0290.04152.6

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
Aimless0.5.26data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BUQ

5buq


Resolution: 1.763→29.957 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.48
RfactorNum. reflection% reflection
Rfree0.1935 1994 86 %
Rwork0.1632 --
obs0.1635 230804 92.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.96 Å2 / Biso mean: 29.562 Å2 / Biso min: 7.43 Å2
Refinement stepCycle: final / Resolution: 1.763→29.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14677 0 410 2032 17119
Biso mean--32.72 43.8 -
Num. residues----1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615464
X-RAY DIFFRACTIONf_angle_d0.88321027
X-RAY DIFFRACTIONf_chiral_restr0.0542395
X-RAY DIFFRACTIONf_plane_restr0.0052666
X-RAY DIFFRACTIONf_dihedral_angle_d15.6239217
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 (%)
1.763-1.80710.22971310.2158161041623592
1.8071-1.85590.22691550.2092166061676194
1.8559-1.91050.29981370.2532164971663494
1.9105-1.97220.25751540.2304165381669294
1.9722-2.04270.2021400.1715165801672094
2.0427-2.12440.1961500.1634165951674594
2.1244-2.22110.20651420.1669165681671094
2.2211-2.33820.22191500.1975165261667694
2.3382-2.48460.21761370.1651165851672294
2.4846-2.67630.19411480.1574164941664294
2.6763-2.94540.191460.1535164141656093
2.9454-3.37110.1821350.1483162991643493
3.3711-4.24530.14161380.1299158261596490
4.2453-29.96080.18941310.1549151781530986
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)
10.8110.0546-0.17780.7759-0.69231.2665-0.0085-0.0698-0.07080.01-0.1141-0.15940.12260.2368-0.04530.14060.0251-0.0020.1156-0.00660.0982120.37510.2179-88.8967
20.34620.1667-0.11780.4106-0.56250.81820.0531-0.10010.10410.1629-0.03990.0977-0.2764-0.05970.02260.22260.01310.02470.0929-0.06060.1213107.022517.0948-86.1804
30.49730.00290.15850.3197-0.46920.72220.0220.13510.1093-0.04490.07970.08310.0679-0.19940.00890.15-0.0091-0.00790.1483-0.00230.141897.3347.878-104.4701
40.3121-0.1251-0.05340.3120.13580.55040.0758-0.2534-0.0598-0.08180.01690.25440.1364-0.43980.00220.2016-0.0932-0.02460.33260.03320.212187.8903-6.7528-82.5902
51.0775-0.30470.45320.7806-0.4580.83990.0262-0.08-0.08280.11130.06940.07210.0116-0.11420.10840.1118-0.00720.01140.0711-0.01990.098597.7791-29.0159-113.8624
60.3549-0.15270.20140.522-0.36380.40230.21010.4756-0.0055-0.1596-0.1811-0.10520.19790.42080.04570.18310.0997-0.02040.1763-0.16530.0515108.9142-34.2739-132.4889
70.4998-0.08-0.05960.7073-0.58290.5603-0.06340.20430.36380.1278-0.1417-0.2955-0.07530.1545-0.06470.0951-0.036-0.00660.20280.05040.2133118.9834-14.5116-127.3952
80.4812-0.0897-0.06960.51850.22670.41110.09150.1317-0.09730.16660.0005-0.42680.02310.25610.02740.1745-0.0043-0.09850.2025-0.03560.3511131.3325-32.852-110.3192
90.9603-0.11610.04830.6916-0.2180.67720.03360.26970.0854-0.1458-0.02010.07560.0488-0.0449-0.00780.14670.0106-0.02250.1710.02270.1397116.962825.3027-126.6895
100.57320.0040.0110.7124-0.2340.4212-0.0363-0.0030.1110.1139-0.0225-0.0782-0.06040.0675-0.02460.1376-0.0105-0.02010.09080.01140.1735128.151632.2552-108.0342
110.4316-0.24750.11370.3417-0.4350.64270.00070.0398-0.11040.0119-0.063-0.07180.01340.153400.09910.01690.01480.15710.01550.1625140.375513.908-109.965
120.05850.09640.11850.50350.3970.42080.13110.32310.3432-0.0332-0.0451-0.2610.03320.07630.10310.13440.00780.0830.30440.12460.3257150.996630.5661-129.8995
130.6407-0.16670.28310.7452-0.16140.7471-0.05840.09220.2074-0.0263-0.0222-0.1016-0.14330.0997-0.07720.1384-0.0345-00.1640.05260.179797.10512.9508-144.3107
140.39260.06020.39270.32430.03780.76040.01340.12250.0261-0.063-0.00920.04280.0740.0287-0.00510.137-0.00850.01050.17350.00940.078786.486-15.6956-150.9143
150.4207-0.27110.31440.448-0.45970.461-0.0754-0.174-0.00850.09450.210.1725-0.0599-0.32150.0540.09050.02360.04160.28070.04670.158575.8654-11.6955-130.7386
160.36810.24380.1040.28130.26320.318-0.07980.13210.311-0.0854-0.10260.2907-0.2095-0.375-0.05750.21610.1219-0.06320.37020.01520.340663.62045.6048-149.1551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:188)A2 - 188
2X-RAY DIFFRACTION2(chain A and resid 189:303)A189 - 303
3X-RAY DIFFRACTION3(chain A and resid 304:385)A304 - 385
4X-RAY DIFFRACTION4(chain A and resid 386:485)A386 - 485
5X-RAY DIFFRACTION5(chain B and resid 2:181)B2 - 181
6X-RAY DIFFRACTION6(chain B and resid 182:302)B182 - 302
7X-RAY DIFFRACTION7(chain B and resid 303:383)B303 - 383
8X-RAY DIFFRACTION8(chain B and resid 384:486)B384 - 486
9X-RAY DIFFRACTION9(chain C and resid 2:162)C2 - 162
10X-RAY DIFFRACTION10(chain C and resid 163:305)C163 - 305
11X-RAY DIFFRACTION11(chain C and resid 306:381)C306 - 381
12X-RAY DIFFRACTION12(chain C and resid 382:486)C382 - 486
13X-RAY DIFFRACTION13(chain D and resid 2:181)D2 - 181
14X-RAY DIFFRACTION14(chain D and resid 182:302)D182 - 302
15X-RAY DIFFRACTION15(chain D and resid 303:382)D303 - 382
16X-RAY DIFFRACTION16(chain D and resid 383:485)D383 - 485

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