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- PDB-7eby: Crystal structure of D-Succinylase (DSA) from Cupriavidus sp. P4-10-C -

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Basic information

Entry
Database: PDB / ID: 7eby
TitleCrystal structure of D-Succinylase (DSA) from Cupriavidus sp. P4-10-C
ComponentsD-succinylase
KeywordsHYDROLASE / D-Succinylase / Cupriavidus sp. P4-10-C / LYASE
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
CARBONATE ION / D-succinylase
Similarity search - Component
Biological speciesCupriavidus sp. P4-10-C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYamasaki, M. / Sumida, Y.
CitationJournal: Adv.Synth.Catal. / Year: 2021
Title: Protein Engineering of d-Succinylase from Cupriavidus sp. for d-Amino Acid Synthesis and the Structural Implications.
Authors: Sumida, Y. / Yamasaki, M. / Nishiya, Y. / Kumagai, S. / Yamada, T. / Azuma, M.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-succinylase
B: D-succinylase
C: D-succinylase
D: D-succinylase
E: D-succinylase
F: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)548,18351
Polymers544,9296
Non-polymers3,25545
Water47,7582651
1
A: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4109
Polymers90,8211
Non-polymers5888
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1346
Polymers90,8211
Non-polymers3125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4109
Polymers90,8211
Non-polymers5888
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,50210
Polymers90,8211
Non-polymers6819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2267
Polymers90,8211
Non-polymers4046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,50210
Polymers90,8211
Non-polymers6819
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.586, 92.117, 162.111
Angle α, β, γ (deg.)94.792, 96.312, 104.902
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 33 or resid 35...
d_2ens_1(chain "B" and (resid 16 through 33 or resid 35...
d_3ens_1(chain "C" and (resid 16 through 33 or resid 35...
d_4ens_1(chain "D" and (resid 16 through 33 or resid 35...
d_5ens_1(chain "E" and (resid 16 through 33 or resid 35...
d_6ens_1(chain "F" and (resid 16 through 33 or resid 35...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRASPA1 - 18
d_12ens_1TRPTYRA20 - 80
d_13ens_1GLYALAA82 - 99
d_14ens_1ALAPROA101 - 121
d_15ens_1GLUTRPA123 - 134
d_16ens_1ALAALAA136 - 169
d_17ens_1ALALEUA171 - 255
d_18ens_1ALALEUA257 - 260
d_19ens_1VALPROA262 - 451
d_110ens_1THRSERA453 - 483
d_111ens_1ALAALAA485
d_112ens_1ARGLYSA487 - 489
d_113ens_1LEUPHEA491 - 568
d_114ens_1ASNGLUA570 - 629
d_115ens_1ARGSERA631 - 744
d_116ens_1LYSVALA746 - 748
d_117ens_1ARGILEA750 - 756
d_118ens_1LEUARGA758 - 761
d_21ens_1THRASPB1 - 18
d_22ens_1TRPTYRB20 - 80
d_23ens_1GLYALAB82 - 99
d_24ens_1ALAPROB101 - 121
d_25ens_1GLUTRPB123 - 134
d_26ens_1ALAALAB136 - 169
d_27ens_1ALALEUB171 - 255
d_28ens_1ALALEUB257 - 260
d_29ens_1VALPROB262 - 451
d_210ens_1THRSERB453 - 483
d_211ens_1ALAALAB485
d_212ens_1ARGLYSB487 - 489
d_213ens_1LEUPHEB491 - 568
d_214ens_1ASNGLUB570 - 629
d_215ens_1ARGSERB631 - 744
d_216ens_1LYSVALB746 - 748
d_217ens_1ARGILEB750 - 756
d_218ens_1LEUARGB758 - 761
d_31ens_1THRASPC2 - 19
d_32ens_1TRPTYRC21 - 81
d_33ens_1GLYALAC83 - 100
d_34ens_1ALAPROC102 - 122
d_35ens_1GLUTRPC124 - 135
d_36ens_1ALAALAC137 - 170
d_37ens_1ALALEUC172 - 256
d_38ens_1ALALEUC258 - 261
d_39ens_1VALPROC263 - 452
d_310ens_1THRSERC454 - 484
d_311ens_1ALAALAC486
d_312ens_1ARGLYSC488 - 490
d_313ens_1LEUPHEC492 - 569
d_314ens_1ASNGLUC571 - 630
d_315ens_1ARGSERC632 - 745
d_316ens_1LYSVALC747 - 749
d_317ens_1ARGILEC751 - 757
d_318ens_1LEUARGC759 - 762
d_41ens_1THRASPD2 - 19
d_42ens_1TRPTYRD21 - 81
d_43ens_1GLYALAD83 - 100
d_44ens_1ALAPROD102 - 122
d_45ens_1GLUTRPD124 - 135
d_46ens_1ALAALAD137 - 170
d_47ens_1ALALEUD172 - 256
d_48ens_1ALALEUD258 - 261
d_49ens_1VALPROD263 - 452
d_410ens_1THRSERD454 - 484
d_411ens_1ALAALAD486
d_412ens_1ARGLYSD488 - 490
d_413ens_1LEUPHED492 - 569
d_414ens_1ASNGLUD571 - 630
d_415ens_1ARGSERD632 - 745
d_416ens_1LYSVALD747 - 749
d_417ens_1ARGILED751 - 757
d_418ens_1LEUARGD759 - 762
d_51ens_1THRASPE2 - 19
d_52ens_1TRPTYRE21 - 81
d_53ens_1GLYALAE83 - 100
d_54ens_1ALAPROE102 - 122
d_55ens_1GLUTRPE124 - 135
d_56ens_1ALAALAE137 - 170
d_57ens_1ALALEUE172 - 256
d_58ens_1ALALEUE258 - 261
d_59ens_1VALPROE263 - 452
d_510ens_1THRSERE454 - 484
d_511ens_1ALAALAE486
d_512ens_1ARGLYSE488 - 490
d_513ens_1LEUPHEE492 - 569
d_514ens_1ASNGLUE571 - 630
d_515ens_1ARGSERE632 - 745
d_516ens_1LYSVALE747 - 749
d_517ens_1ARGILEE751 - 757
d_518ens_1LEUARGE759 - 762
d_61ens_1THRASPF1 - 18
d_62ens_1TRPTYRF20 - 80
d_63ens_1GLYALAF82 - 99
d_64ens_1ALAPROF101 - 121
d_65ens_1GLUTRPF123 - 134
d_66ens_1ALAALAF136 - 169
d_67ens_1ALALEUF171 - 255
d_68ens_1ALALEUF257 - 260
d_69ens_1VALPROF262 - 451
d_610ens_1THRSERF453 - 483
d_611ens_1ALAALAF485
d_612ens_1ARGLYSF487 - 489
d_613ens_1LEUPHEF491 - 568
d_614ens_1ASNGLUF570 - 629
d_615ens_1ARGSERF631 - 744
d_616ens_1LYSVALF746 - 748
d_617ens_1ARGILEF750 - 756
d_618ens_1LEUARGF758 - 761

NCS oper:
IDCodeMatrixVector
1given(-0.996861390973, 0.0180150499848, 0.0770897215065), (0.0493847692801, -0.61956595567, 0.783389539844), (0.0618749686954, 0.784737844473, 0.616731711282)74.7157734297, -71.8430342109, 31.7150644503
2given(0.99921097275, -0.0125355989061, -0.0376867442887), (0.011325969031, 0.999419174238, -0.0321408865983), (0.0380677601196, 0.0316886876642, 0.998772583081)41.4392307914, -23.8119418369, -52.8851433878
3given(-0.999294605836, -0.00765790895454, 0.0367647545421), (0.0335466549587, -0.622057138866, 0.782252860607), (0.0168793568356, 0.78293439854, 0.62187524062)115.775835344, -95.2227152647, -19.410706208
4given(-0.999902109742, -0.0041511304022, 0.0133618505573), (0.0125838514109, -0.684302076108, 0.729090059813), (0.00611699416375, 0.729186832541, 0.684287326809)117.997361396, -48.2456275979, 84.1796656426
5given(0.997976542646, -0.0147301767151, -0.0618533929756), (0.00906897433613, 0.99582524369, -0.0908286173705), (0.0629330917177, 0.0900838827032, 0.993943821372)43.5153634318, 24.7829558112, 54.4279924433

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Components

#1: Protein
D-succinylase


Mass: 90821.445 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus sp. P4-10-C (bacteria) / Gene: DSA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7KZ58
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CO3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2651 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 1500, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 303340 / % possible obs: 97.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 21.13 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rpim(I) all: 0.076 / Rrim(I) all: 0.12 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 15023 / CC1/2: 0.663 / CC star: 0.893 / Rpim(I) all: 0.379 / Rrim(I) all: 0.602 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DENZOdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HST.pdb

4hst


Resolution: 2→47.63 Å / SU ML: 0.2875 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.6881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 15029 5 %
Rwork0.204 285660 -
obs0.2064 300689 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.56 Å2
Refinement stepCycle: LAST / Resolution: 2→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35694 0 204 2651 38549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007537057
X-RAY DIFFRACTIONf_angle_d0.935550510
X-RAY DIFFRACTIONf_chiral_restr0.05775278
X-RAY DIFFRACTIONf_plane_restr0.00916689
X-RAY DIFFRACTIONf_dihedral_angle_d12.150513428
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.46931830285
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.457393779558
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.511174257871
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.442463937978
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.472704511204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.33374810.28439139X-RAY DIFFRACTION92.46
2.02-2.040.32755040.2679569X-RAY DIFFRACTION95.68
2.04-2.070.30244990.25389509X-RAY DIFFRACTION96.06
2.07-2.090.31565050.25319578X-RAY DIFFRACTION95.89
2.09-2.120.33034960.25229434X-RAY DIFFRACTION96.1
2.12-2.150.30265090.24279659X-RAY DIFFRACTION96.13
2.15-2.180.30375000.23939505X-RAY DIFFRACTION96.21
2.18-2.210.30515050.23929600X-RAY DIFFRACTION96.15
2.21-2.250.28615040.22889562X-RAY DIFFRACTION96.03
2.25-2.280.29715040.23249574X-RAY DIFFRACTION96.27
2.28-2.320.29335030.22159569X-RAY DIFFRACTION96.48
2.32-2.370.28485050.21769593X-RAY DIFFRACTION96.43
2.37-2.410.2865030.21679560X-RAY DIFFRACTION96.48
2.41-2.460.30985060.22579615X-RAY DIFFRACTION96.57
2.46-2.510.27315030.21959546X-RAY DIFFRACTION96.54
2.51-2.570.29535090.22199673X-RAY DIFFRACTION96.55
2.57-2.640.29345050.22459597X-RAY DIFFRACTION96.58
2.64-2.710.27635050.21559599X-RAY DIFFRACTION96.67
2.71-2.790.275070.21519623X-RAY DIFFRACTION96.49
2.79-2.880.29995050.21979587X-RAY DIFFRACTION96.52
2.88-2.980.27045060.219627X-RAY DIFFRACTION96.74
2.98-3.10.2545030.20769570X-RAY DIFFRACTION96.34
3.1-3.240.25145020.20839534X-RAY DIFFRACTION95.97
3.24-3.410.23534990.19659490X-RAY DIFFRACTION95.56
3.41-3.630.22734940.19249378X-RAY DIFFRACTION94.5
3.63-3.90.20634980.17579471X-RAY DIFFRACTION95.32
3.9-4.30.19955000.16869487X-RAY DIFFRACTION95.35
4.3-4.920.1774940.14869381X-RAY DIFFRACTION94.14
4.92-6.20.18344970.16659446X-RAY DIFFRACTION95.11
6.2-47.630.18454780.16869185X-RAY DIFFRACTION92.33

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