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- PDB-2a5h: 2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase fr... -

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Basic information

Entry
Database: PDB / ID: 2a5h
Title2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).
ComponentsL-lysine 2,3-aminomutase
KeywordsISOMERASE / radical sam / four-iron-four-sulfur cluster / 4Fe4S / FS4 / SAM / S-adenosylmethionine / alpha-beta channel / pyridoxal-5'-phosphate / external aldimine / Michaelis analog
Function / homology
Function and homology information


lysine 2,3-aminomutase / L-lysine 2,3-aminomutase activity / L-lysine catabolic process to acetate / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Helix Hairpins - #1170 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Lysine-2,3-aminomutase/glutamate 2,3-aminomutase / Lysine-2,3-aminomutase / Lysine-2,3-aminomutase, C-terminal domain / Lysine-2,3-aminomutase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM ...Helix Hairpins - #1170 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Lysine-2,3-aminomutase/glutamate 2,3-aminomutase / Lysine-2,3-aminomutase / Lysine-2,3-aminomutase, C-terminal domain / Lysine-2,3-aminomutase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Other non-globular / Helix Hairpins / Helix non-globular / Special / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
LYSINE / PYRIDOXAL-5'-PHOSPHATE / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / : / L-lysine 2,3-aminomutase
Similarity search - Component
Biological speciesClostridium subterminale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLepore, B.W. / Ruzicka, F.J. / Frey, P.A. / Ringe, D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale.
Authors: Lepore, B.W. / Ruzicka, F.J. / Frey, P.A. / Ringe, D.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Remark 7ATOMS WITH ZERO OCCUPANCY: -------------------------- 90 ATOMS WERE NOT SUFFICIENTLY ORDERED IN THE ...ATOMS WITH ZERO OCCUPANCY: -------------------------- 90 ATOMS WERE NOT SUFFICIENTLY ORDERED IN THE CRYSTAL TO CONTRIBUTE SIGNIFICANTLY TO THE FOURIER MAP. THESE ATOMS WERE SET TO ZERO OCCUPANCY AND HAD THEIR B-EQ'S AND ANISOU EIGENVALUES SET TO ZERO. TABLE OF ATOMS WITH ZERO OCCUPANCY: ----------------------------------- +-----------------------------------------------------+ | RESIDUE | CHAIN | RESID | ATOMS | |-----------|---------|------ |-----------------------| | LYSINE | A/ /C/ | 10 | CG, CD,CE AND NZ | | GLUTAMATE | A/B/ / | 33 | CD, OE1 AND OE2 | | LYSINE | A/B/C/D | 42 | CD, CE AND NZ | | GLUTAMATE | A/B/C/ | 43 | CG, CD, OE1 AND OE2 | | GLUTAMATE | A/B/C/D | 46 | CD, OE1 AND OE2 | | GLUTAMATE | A/ /C/D | 148 | CD, OE1 AND OE2. | | GLUTAMATE | A/B/C/D | 239 | CD, OE1 AND OE2. | | LYSINE | A/B/C/D | 385 | CD, CE, AND NZ. | | GLUTAMATE | A/B/ /D | 408 | OE1 AND OE2. | +-----------------------------------------------------+
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 1 .. 417 B 1 .. 417 ? M 2 A 1 .. 417 C 1 .. 417 ? M 3 A 1 .. 417 D 1 .. 417 ? WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK:

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lysine 2,3-aminomutase
B: L-lysine 2,3-aminomutase
C: L-lysine 2,3-aminomutase
D: L-lysine 2,3-aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,76328
Polymers190,5404
Non-polymers5,22424
Water10,953608
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32280 Å2
ΔGint-474 kcal/mol
Surface area52150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.890, 92.926, 177.735
Angle α, β, γ (deg.)90.00, 96.74, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D
331A
341B
351C
361D
371A
381B
391C
401D
411A
421B
431C
441D
451A
461B
471C
481D
491A
501B
511C
521D
531A
541B
551C
561D
571A
581B
591C
601D
611A
621B
631C
641D
651A
661B
671C
681D
691A
701B
711C
721D
731A
741B
751C
761D
771A
781B
791C
801D
811A
821B
831C
841D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNPHE1AA3 - 93 - 9
21ASNPHE1BB3 - 93 - 9
31ASNPHE1CC3 - 93 - 9
41ASNPHE1DD3 - 93 - 9
52LYSLYS3AA1010
62LYSLYS3BB1010
72LYSLYS3CC1010
82LYSLYS3DD1010
93ASPTHR1AA11 - 3011 - 30
103ASPTHR1BB11 - 3011 - 30
113ASPTHR1CC11 - 3011 - 30
123ASPTHR1DD11 - 3011 - 30
134VALVAL3AA3131
144VALVAL3BB3131
154VALVAL3CC3131
164VALVAL3DD3131
175GLUGLU1AA3232
185GLUGLU1BB3232
195GLUGLU1CC3232
205GLUGLU1DD3232
216GLUGLU3AA3333
226GLUGLU3BB3333
236GLUGLU3CC3333
246GLUGLU3DD3333
257LEUTHR1AA34 - 4134 - 41
267LEUTHR1BB34 - 4134 - 41
277LEUTHR1CC34 - 4134 - 41
287LEUTHR1DD34 - 4134 - 41
298LYSGLU3AA42 - 4342 - 43
308LYSGLU3BB42 - 4342 - 43
318LYSGLU3CC42 - 4342 - 43
328LYSGLU3DD42 - 4342 - 43
339GLUGLU1AA44 - 4544 - 45
349GLUGLU1BB44 - 4544 - 45
359GLUGLU1CC44 - 4544 - 45
369GLUGLU1DD44 - 4544 - 45
3710GLUGLU3AA4646
3810GLUGLU3BB4646
3910GLUGLU3CC4646
4010GLUGLU3DD4646
4111GLYMSE1AA47 - 14747 - 147
4211GLYMSE1BB47 - 14747 - 147
4311GLYMSE1CC47 - 14747 - 147
4411GLYMSE1DD47 - 14747 - 147
4512GLUGLU3AA148148
4612GLUGLU3BB148148
4712GLUGLU3CC148148
4812GLUGLU3DD148148
4913ARGTHR1AA149 - 238149 - 238
5013ARGTHR1BB149 - 238149 - 238
5113ARGTHR1CC149 - 238149 - 238
5213ARGTHR1DD149 - 238149 - 238
5314GLUGLU3AA239239
5414GLUGLU3BB239239
5514GLUGLU3CC239239
5614GLUGLU3DD239239
5715GLULYS1AA240 - 384240 - 384
5815GLULYS1BB240 - 384240 - 384
5915GLULYS1CC240 - 384240 - 384
6015GLULYS1DD240 - 384240 - 384
6116LYSLYS3AA385385
6216LYSLYS3BB385385
6316LYSLYS3CC385385
6416LYSLYS3DD385385
6517VALLEU1AA386 - 407386 - 407
6617VALLEU1BB386 - 407386 - 407
6717VALLEU1CC386 - 407386 - 407
6817VALLEU1DD386 - 407386 - 407
6918GLUGLU3AA408408
7018GLUGLU3BB408408
7118GLUGLU3CC408408
7218GLUGLU3DD408408
7319ARGLYS1AA409 - 411409 - 411
7419ARGARG1BB409 - 412409 - 412
7519ARGLYS1CC409 - 411409 - 411
7619ARGARG1DD409 - 412409 - 412
7720PLPLYS1AQ419 - 420
7820PLPLYS1BR419 - 420
7920PLPLYS1CS419 - 420
8020PLPLYS1DT419 - 420
8121SAMSF41AM - U417 - 418
8221SAMSF41BN - V417 - 418
8321SAMSF41CO - W417 - 418
8421SAMSF41DP - X417 - 418

NCS oper:
IDCodeMatrixVector
1given(-0.8655, 0.09092, 0.49258), (0.09126, -0.93831, 0.33353), (0.49252, 0.33363, 0.80382)-21.66147, 29.14558, 0.50866
2given(0.86148, 0.00258, -0.50778), (-6.0E-5, -0.99999, -0.00519), (-0.50779, 0.0045, -0.86147)-25.32914, 12.64268, -93.10329
3given(-0.99547, -0.09351, 0.01705), (-0.09376, 0.93656, -0.33773), (0.01562, -0.3378, -0.94109)-44.17323, -16.50383, -82.41089
Detailsasymmetric unit contains the tetrameric biologically relevant assembly. considering chain A, we construct the asymmetric unit from the following symmetry operators: chain A <-> A (identity) rotation matrix: 1 0 0 0 1 0 0 0 1 translation: 0 0 0 chain A <-> B rotation matrix -0.86550 0.09092 0.49258 0.09126 -0.93831 0.33353 0.49252 0.33363 0.80382 translation: -21.66147 29.14558 0.50866 chain A <-> C rotation matrix: 0.86148 0.00258 -0.50778 -0.00006 -0.99999 -0.00519 -0.50779 0.00450 -0.86147 translation: -25.32914 12.64268 -93.10329 chain A <-> D -0.99547 -0.09351 0.01705 -0.09376 0.93656 -0.33773 0.01562 -0.33780 -0.94109 translation: -44.17323 -16.50383 -82.41089

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-lysine 2,3-aminomutase


Mass: 47634.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium subterminale (bacteria) / Gene: KamA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL-X
References: GenBank: 5410603, UniProt: Q9XBQ8*PLUS, lysine 2,3-aminomutase

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Non-polymers , 7 types, 632 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical
ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#7: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6753.88
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
3001vapor diffusion, sitting drop8sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K
3002vapor diffusion, hanging drop8sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9742
SYNCHROTRONAPS 17-ID20.9792
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 9, 2003monochromator with Si (111) crystal
ADSC QUANTUM 42CCDMar 28, 2003monochromator with Si(111) double-crystal
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97421
20.97921
ReflectionResolution: 2.1→50 Å / Num. all: 83957 / Num. obs: 83957 / % possible obs: 81.53 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.97 / Rsym value: 0.265 / % possible all: 62.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASS/OPTIX (AT X25)data collection
MXdata reduction
JBluIce-EPICSdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.228 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22485 7437 8.1 %RANDOM
Rwork0.18396 ---
obs0.18732 83957 81.53 %-
all-83957 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.824 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-1.71 Å2
2--3.3 Å20 Å2
3----4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12990 0 264 608 13862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0862.01218806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1851642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99323.059608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.343152342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.77415135
X-RAY DIFFRACTIONr_chiral_restr0.1770.22088
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210219
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.26617
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.29124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2803
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3820.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3930.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5821.58460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.861213493
X-RAY DIFFRACTIONr_scbond_it1.63535902
X-RAY DIFFRACTIONr_scangle_it2.3624.55073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3274tight positional0.050.05
2B3274tight positional0.060.05
3C3274tight positional0.060.05
4D3274tight positional0.060.05
1A20loose positional0.365
2B20loose positional0.335
3C20loose positional0.225
4D20loose positional0.285
1A3274tight thermal0.170.5
2B3274tight thermal0.170.5
3C3274tight thermal0.180.5
4D3274tight thermal0.160.5
1A20loose thermal0.910
2B20loose thermal1.6710
3C20loose thermal1.610
4D20loose thermal0.7810
LS refinement shellResolution: 2.1→2.213 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 690 -
Rwork0.25 7986 -
obs--53.25 %
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)
11.21250.03570.01620.74680.13362.80390.0672-0.35540.0280.1091-0.0177-0.0513-0.13220.3226-0.0495-0.1241-0.022-0.024-0.0799-0.0176-0.1753-16.702510.6572-21.5786
21.1763-0.0290.00310.75370.12692.31270.03870.1028-0.0911-0.06070.0341-0.00780.104-0.1444-0.0728-0.1785-0.0142-0.006-0.2806-0.0126-0.1781-28.83472.2011-65.9553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA - E3 - 4213
2X-RAY DIFFRACTION1BB - G3 - 4213
3X-RAY DIFFRACTION2CC - I3 - 4213
4X-RAY DIFFRACTION2DD - K3 - 4213

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