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- PDB-4a72: Crystal structure of the omega transaminase from Chromobacterium ... -

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Basic information

Entry
Database: PDB / ID: 4a72
TitleCrystal structure of the omega transaminase from Chromobacterium violaceum in a mixture of apo and PLP-bound states
ComponentsOMEGA TRANSAMINASE
KeywordsTRANSFERASE / PLP-BINDING ENZYME / TRANSAMINASE FOLD TYPE I
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
PYRIDOXAL-5'-PHOSPHATE / Putative 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesCHROMOBACTERIUM VIOLACEUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLogan, D.T. / Hakansson, M. / Yengo, K. / Svedendahl Humble, M. / Engelmark Cassimjee, K. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P.
CitationJournal: FEBS J. / Year: 2012
Title: Crystal Structures of the Chromobacterium Violaceum Omega-Transaminase Reveal Major Structural Rearrangements Upon Binding of Coenzyme Plp.
Authors: Svedendahl Humble, M. / Engelmark Cassimjee, K. / Hakansson, M. / Kimbung, Y.R. / Walse, B. / Abedi, V. / Federsel, H.-J. / Berglund, P. / Logan, D.T.
History
DepositionNov 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OMEGA TRANSAMINASE
B: OMEGA TRANSAMINASE
C: OMEGA TRANSAMINASE
D: OMEGA TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,6116
Polymers205,1174
Non-polymers4942
Water9,512528
1
A: OMEGA TRANSAMINASE
B: OMEGA TRANSAMINASE


Theoretical massNumber of molelcules
Total (without water)102,5592
Polymers102,5592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-51.4 kcal/mol
Surface area30170 Å2
MethodPISA
2
C: OMEGA TRANSAMINASE
D: OMEGA TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0534
Polymers102,5592
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-73.1 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.350, 62.120, 119.240
Angle α, β, γ (deg.)105.27, 90.66, 104.43
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.08323, -0.9675, -0.2387), (-0.9613, -0.1411, 0.2367), (-0.2626, 0.2098, -0.9418)-37.88, -22.15, -78.44
2given(0.9776, -0.1988, 0.06912), (0.197, 0.9799, 0.03139), (-0.07397, -0.01706, 0.9971)-0.2474, -10.84, 55.49
3given(0.2532, -0.894, -0.3695), (-0.9337, -0.3258, 0.1483), (-0.253, 0.3075, -0.9173)-39.53, -43.38, -19.23

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Components

#1: Protein
OMEGA TRANSAMINASE


Mass: 51279.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7NWG4, beta-alanine-pyruvate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE
Crystal growpH: 7.4
Details: 200 NL OF PROTEIN AT 12 MG/ML IN 1 MM CYCLOSERINE MIXED WITH 200 NL OF RESERVOIR CONSISTING OF 0.1 M HEPES PH 7.5, 150-300 MM NACL AND 22.5-27.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 6, 2011 / Details: MULTILAYER MIRROR, VERTICALLY FOCUSING
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 61839 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 27.53 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 82.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A6R

4a6r


Resolution: 2.4→26.391 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2394 3139 5.1 %
Rwork0.1729 --
obs0.1763 61746 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.401 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.487 Å24.6434 Å22.0306 Å2
2---1.734 Å2-4.874 Å2
3----2.753 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13841 0 30 528 14399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214235
X-RAY DIFFRACTIONf_angle_d0.63919265
X-RAY DIFFRACTIONf_dihedral_angle_d12.7325141
X-RAY DIFFRACTIONf_chiral_restr0.0382003
X-RAY DIFFRACTIONf_plane_restr0.0022514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43750.33351470.23452541X-RAY DIFFRACTION92
2.4375-2.47740.30971170.23812688X-RAY DIFFRACTION96
2.4774-2.52010.38171320.23372624X-RAY DIFFRACTION96
2.5201-2.56590.37951270.23642674X-RAY DIFFRACTION96
2.5659-2.61520.3461400.21782651X-RAY DIFFRACTION96
2.6152-2.66850.32311620.22042631X-RAY DIFFRACTION96
2.6685-2.72650.30481200.21022676X-RAY DIFFRACTION96
2.7265-2.78980.28761200.21082723X-RAY DIFFRACTION97
2.7898-2.85950.28591420.19642626X-RAY DIFFRACTION96
2.8595-2.93680.27691550.18752677X-RAY DIFFRACTION97
2.9368-3.02310.25381660.17792646X-RAY DIFFRACTION97
3.0231-3.12050.25911250.17932710X-RAY DIFFRACTION97
3.1205-3.23180.22651390.17332706X-RAY DIFFRACTION97
3.2318-3.3610.24271470.17332654X-RAY DIFFRACTION97
3.361-3.51360.26591560.17452684X-RAY DIFFRACTION97
3.5136-3.69840.23391640.1732658X-RAY DIFFRACTION97
3.6984-3.92940.20161400.14522685X-RAY DIFFRACTION97
3.9294-4.23170.19551450.13932699X-RAY DIFFRACTION97
4.2317-4.65540.17721660.12892659X-RAY DIFFRACTION97
4.6554-5.32420.19891430.14072670X-RAY DIFFRACTION97
5.3242-6.68990.20561470.16312691X-RAY DIFFRACTION97
6.6899-26.39270.16871390.15432634X-RAY DIFFRACTION95
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)
13.28370.20091.00772.73820.99432.14510.0266-0.0471-0.21620.04210.0642-0.36510.15920.3163-0.06730.16150.10550.04170.24040.00080.0893-10.3192-20.0517-49.2459
22.35920.03940.84962.47760.86632.57260.0621-0.00380.01390.09290.00940.18150.1222-0.2128-0.06370.0552-0.00610.0090.09970.01950.0419-35.1787-4.6068-51.4599
32.2846-1.25810.24341.20410.38910.56420.10890.301-0.0174-0.1664-0.0968-0.0146-0.0330.0958-0.01730.15880.00350.02160.2240.01390.0971-24.4224-8.3888-57.9926
42.4577-3.30450.03444.7568-0.29940.2032-0.05010.13890.61520.14670.0349-0.8153-0.15020.0609-0.04450.09960.00230.01090.3042-0.00650.2988-10.3339-5.8294-50.7229
52.6607-0.6268-0.08031.56380.38041.8747-0.07210.1517-0.67840.0278-0.01180.35130.6362-0.17090.08510.3589-0.0179-0.02330.1376-0.10040.2754-35.8458-31.149-58.0054
61.27680.00470.39471.51310.96461.2919-0.14210.2935-0.2385-0.07750.1086-0.01540.12840.21060.02790.10250.10750.09010.191-0.04820.1122-4.7059-20.5573-35.1819
73.1064-0.2841-1.11323.3011.40591.603-0.00330.2995-0.2915-0.0219-0.08970.13120.0588-0.18630.06690.08130.0163-0.01570.22340.01530.1012-27.0676-10.3421-26.7616
86.25332.5034.05442.60642.4943.228-0.30330.57030.4457-0.38960.12520.0972-0.68790.19680.15710.18350.04010.01810.17290.02310.1031-20.04126.3821-24.1297
91.2262-0.78-0.4672.15821.1072.00220.00010.0472-0.07520.0918-0.0291-0.01510.0920.02980.03440.0880.03570.00750.10190.02440.0449-20.6545-7.3822-17.8633
101.9718-1.0087-1.78760.61410.77621.8173-0.10890.4177-0.74080.0212-0.28530.78910.1128-0.71830.24640.20910.04680.02520.2893-0.16490.4742-17.6641-24.1942-31.388
111.7169-0.0416-0.50522.86440.111.63650.0877-0.00630.10890.12230.0225-0.187-0.26250.4098-0.10440.0789-0.0215-0.00530.3156-0.00320.12351.05321.8916-20.345
122.5247-1.1564-0.39385.03820.48293.21640.15650.27260.4929-0.4428-0.0547-0.5484-0.69630.7276-0.01010.2129-0.12380.02340.45790.0370.23999.80396.6677-22.7704
130.6734-0.03670.35021.85960.38312.9308-0.0101-0.2454-0.15320.38760.02410.00490.26760.0199-0.01550.20480.0510.01490.1190.04940.1274-20.0023-50.107318.7218
141.72530.53220.66232.98180.64912.386-0.0790.11280.26940.11040.1851-0.4421-0.20920.4298-0.10140.120.02330.04570.1249-0.00110.2209-4.0709-29.08759.6427
151.1832-0.59310.26311.2936-0.1430.30860.0320.05970.1924-0.23-0.0797-0.37-0.27480.02150.02580.2481-0.00380.03150.08620.0440.1709-21.7704-17.25056.9005
160.7946-0.31930.15682.11140.2851.43520.01080.0011-0.0435-0.1506-0.09720.2209-0.0655-0.25220.02220.17150.0748-0.02840.06980.0270.0448-39.6028-26.48885.2548
171.8358-0.72840.20621.7326-0.34380.53960.0010.01250.13-0.2188-0.0029-0.0874-0.2803-0.05380.01910.28830.0160.0290.07750.01290.1049-22.4941-23.06873.4519
183.28771.27610.07781.72980.53461.53590.00210.2669-0.0319-0.1731-0.07070.14530.0576-0.26380.07210.15940.0794-0.00720.0435-0.00220.1035-30.6463-45.2662-1.1316
196.3824-2.7233-0.73291.18620.32990.17830.0823-0.5573-0.03820.3514-0.05080.2607-0.12990.0334-0.06710.2282-0.05810.02280.1132-0.00780.1862-29.7449-49.42557.3232
203.469-0.3279-1.59541.87120.07412.265-0.15470.236-0.7381-0.0024-0.02150.27620.3921-0.22320.23670.22670.00530.00480.1216-0.07680.2143-31.482-56.49871.8163
212.9899-0.06571.85040.4363-0.29015.84210.07910.39220.1201-0.3229-0.0004-0.594-0.20250.4747-0.08080.3415-0.01380.16810.162-0.06340.4836-0.9385-15.451112.3998
221.2755-0.5431-0.7761.35710.68621.5605-0.0175-0.13310.12960.30080.0498-0.14660.0780.0597-0.02820.18680.0004-0.01860.08970.00340.0786-20.018-24.498633.3687
230.6126-0.3309-0.44821.4801-0.01931.0756-0.0301-0.29070.36620.3570.1234-0.31970.1120.1751-0.07250.15570.0416-0.09230.1497-0.06430.2335-8.9406-29.270831.4149
241.1757-0.1606-0.53560.97970.19841.13380.2102-0.05550.5430.01760.1423-0.6709-0.34670.35140.07780.2106-0.14150.07120.2355-0.18060.6437-0.2548-5.370431.368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 37:119)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 120:239)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 240:303)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 304:341)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 342:459)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 34:106)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 107:157)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 158:196)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 197:311)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 312:341)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 342:431)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 432:459)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 5:61)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 62:101)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 102:141)
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 142:246)
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 247:327)
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 328:407)
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 408:427)
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 428:458)
21X-RAY DIFFRACTION21CHAIN D AND (RESSEQ 5:61)
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 62:286)
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 287:367)
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 368:458)

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