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- PDB-3wy7: Crystal structure of Mycobacterium smegmatis 7-Keto-8-aminopelarg... -

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Basic information

Entry
Database: PDB / ID: 3wy7
TitleCrystal structure of Mycobacterium smegmatis 7-Keto-8-aminopelargonic acid (KAPA) synthase BioF
Components8-amino-7-oxononanoate synthase
KeywordsTRANSFERASE / domain swapping / alpha and beta / alpha-beta-alpha sandwich / Synthase / pyridoxal 5'-phosphate (PLP) binding
Function / homology
Function and homology information


8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFan, S.H. / Li, D.F. / Wang, D.C. / Chen, G.J. / Zhang, X.E. / Bi, L.J.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2014
Title: Structure and function of Mycobacterium smegmatis 7-keto-8-aminopelargonic acid (KAPA) synthase
Authors: Fan, S.H. / Li, D.F. / Wang, D.C. / Fleming, J. / Zhang, H.T. / Zhou, Y. / Zhou, L. / Zhou, J. / Chen, T. / Chen, G.J. / Zhang, X.E. / Bi, L.J.
History
DepositionAug 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase
C: 8-amino-7-oxononanoate synthase
D: 8-amino-7-oxononanoate synthase


Theoretical massNumber of molelcules
Total (without water)167,7304
Polymers167,7304
Non-polymers00
Water7,404411
1
A: 8-amino-7-oxononanoate synthase
B: 8-amino-7-oxononanoate synthase


Theoretical massNumber of molelcules
Total (without water)83,8652
Polymers83,8652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-19 kcal/mol
Surface area25960 Å2
MethodPISA
2
C: 8-amino-7-oxononanoate synthase
D: 8-amino-7-oxononanoate synthase


Theoretical massNumber of molelcules
Total (without water)83,8652
Polymers83,8652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-23 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.880, 91.680, 109.840
Angle α, β, γ (deg.)90.00, 97.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ALA / End label comp-ID: ALA

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLUchain AAA37 - 38259 - 404
2LEULEUchain BBB12 - 38034 - 402
3GLUGLUchain CCC37 - 38259 - 404
4LEULEUchain DDD12 - 38234 - 404

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Components

#1: Protein
8-amino-7-oxononanoate synthase / / AONS / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7- ...AONS / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase / Alpha-oxoamine synthase


Mass: 41932.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Gene: bioF, MSMEG_3189, MSMEI_3107 / Plasmid: pET28a / Production host: Escherichia coli Bl21(DE3) (bacteria)
References: UniProt: A0QX65, 8-amino-7-oxononanoate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M DL-Malic acid, 20%(w/v) polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2014
RadiationMonochromator: double crystal (Si 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→63.03 Å / Num. all: 61286 / Num. obs: 60733 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 10.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.9 / Num. unique all: 8828 / Rsym value: 0.376 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BS0

1bs0


Resolution: 2.3→55.749 Å / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 28.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 1982 3.26 %RANDOM
Rwork0.2425 ---
all0.2436 61286 --
obs0.2436 60733 97.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.18 Å2 / Biso mean: 40.5292 Å2 / Biso min: 16.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10302 0 0 411 10713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510438
X-RAY DIFFRACTIONf_angle_d1.06614219
X-RAY DIFFRACTIONf_chiral_restr0.041738
X-RAY DIFFRACTIONf_plane_restr0.0061891
X-RAY DIFFRACTIONf_dihedral_angle_d12.313701
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6214X-RAY DIFFRACTION10.559TORSIONAL
12B6214X-RAY DIFFRACTION10.559TORSIONAL
13C6214X-RAY DIFFRACTION10.559TORSIONAL
14D6214X-RAY DIFFRACTION10.559TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.35760.31311310.28673963409493
2.3576-2.42130.32741370.27724142427997
2.4213-2.49260.27561430.26264125426898
2.4926-2.5730.33841430.27344199434298
2.573-2.6650.33691410.27584205434698
2.665-2.77170.31531420.26954209435199
2.7717-2.89780.29251430.26834221436499
2.8978-3.05060.28951430.26294242438599
3.0506-3.24170.31081430.24834232437599
3.2417-3.4920.25441410.2354187432898
3.492-3.84330.24921440.22314244438899
3.8433-4.39920.23251440.21684265440999
4.3992-5.54180.26831440.21234277442199
5.5418-55.76550.26381430.2414240438396
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)
11.252-1.002-0.16820.66950.19333.16970.01740.47350.47940.0198-0.0878-0.5248-0.5604-0.15020.05460.1759-0.03410.05650.55630.1260.48967.7768-18.98416.5077
21.6009-0.71040.23421.3344-0.24781.47710.00210.09580.14350.06-0.0501-0.2510.01890.14620.0670.2603-0.0326-0.01270.32470.06250.297932.2054-20.834414.7566
32.209-0.48860.47110.86390.74411.1668-0.07210.08560.15160.16390.0481-0.0773-0.2174-0.0904-0.01140.2955-0.0422-0.0310.40530.08290.259917.8073-22.321615.5669
40.838-0.04170.79631.78960.75481.33180.06930.4097-0.2067-0.22660.3449-0.80430.02010.6212-0.1360.2954-0.0430.01210.5155-0.10760.675219.1565-46.13684.5046
51.1973-0.49261.62090.161-0.60061.8708-0.5335-1.42940.4080.4216-0.0347-0.284-1.3521-0.39390.18090.6526-0.0824-0.06130.8990.05740.537820.46531.28758.3262
60.57390.71030.13552.0546-0.57072.56410.0445-0.0022-0.7386-0.9424-0.209-1.11050.93490.290.10130.44380.02530.10060.6450.09230.79516.019-22.5739-3.3418
72.09370.4044-0.14871.22620.18851.79230.05860.1836-0.1821-0.1032-0.0956-0.1818-0.08280.28230.05780.26580.06180.06130.44680.12620.324329.6679-11.4663-14.9259
82.36670.32-0.26662.40380.40631.7281-0.0124-0.28960.28990.16840.0548-0.2419-0.01820.1191-0.06170.23530.0543-0.03630.40610.05690.313316.0162-0.0436-8.7369
90.56860.69450.64510.66050.52591.63790.0401-0.47070.67-0.1229-0.2840.3865-0.266-0.25520.01860.25980.00830.05910.301-0.12780.619620.24971.310447.9109
102.03150.53040.26062.3744-0.41350.97840.00250.25820.0444-0.25120.02180.2654-0.0808-0.08140.00440.28730.0458-0.03160.22790.03290.2021-1.0058-1.862337.7984
115.9269-0.14933.39471.7193-0.85112.2745-0.7287-1.23011.02291.56040.48290.6494-1.2786-0.8691-0.44710.80250.19660.19950.38290.07720.39113.410311.390243.796
121.1863-0.28630.44721.8735-0.23611.07920.04710.3654-0.0332-0.1970.23960.11140.0781-0.2729-0.06120.25740.01680.02110.1394-0.02190.224813.6451-16.133240.2295
131.31770.37520.3282.04750.05771.6451-0.1254-0.1978-0.00950.10780.13290.3055-0.0885-0.47790.04250.3027-0.0227-0.00390.33560.0650.303110.9032-25.971550.9403
144.6126-0.1487-1.62030.250.84272.61670.27362.12850.683-0.694-0.55720.2414-1.796-0.83570.58220.5628-0.33350.0327-0.2130.04260.77857.169721.052446.1227
150.9526-0.4488-0.73650.6068-0.50922.255-0.32250.0011-0.9519-0.10550.52011.24530.7878-0.662-0.15120.4353-0.0219-0.03220.4448-0.01820.877521.4016-2.272856.9787
163.7435-0.0191-0.19570.689-0.00561.3841-0.0321-0.329-0.2294-0.00460.02180.14930.2306-0.14570.01260.3444-0.03250.00350.210.07630.23770.97687.160868.525
171.475-0.4261-0.37131.76671.00682.1667-0.07510.07380.35010.1325-0.0260.2438-0.4827-0.25970.02440.2742-0.0245-0.06650.2127-0.01830.435713.207629.003960.977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 37 THROUGH 79 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 80 THROUGH 200 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 201 THROUGH 302 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 303 THROUGH 382 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 12 THROUGH 51 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 52 THROUGH 79 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 80 THROUGH 200 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 201 THROUGH 380 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 37 THROUGH 79 )
10X-RAY DIFFRACTION10CHAIN C AND (RESID 80 THROUGH 241 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 242 THROUGH 268 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 269 THROUGH 322 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 323 THROUGH 382 )
14X-RAY DIFFRACTION14CHAIN D AND (RESID 12 THROUGH 51 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 52 THROUGH 79 )
16X-RAY DIFFRACTION16CHAIN D AND (RESID 80 THROUGH 268 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 269 THROUGH 382 )

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