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- PDB-2bwo: 5-Aminolevulinate Synthase from Rhodobacter capsulatus in complex... -

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Basic information

Entry
Database: PDB / ID: 2bwo
Title5-Aminolevulinate Synthase from Rhodobacter capsulatus in complex with succinyl-CoA
Components5-AMINOLEVULINATE SYNTHASE
KeywordsTRANSFERASE / TETRAPYRROLE BIOSYNTHESIS / HEME BIOSYNTHESIS / PYRIDOXAL PHOSPHATE DEPENDENT / ACYLTRANSFERASE
Function / homology
Function and homology information


5-aminolevulinate synthase / 5-aminolevulinate synthase activity / hemoglobin biosynthetic process / protoporphyrinogen IX biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase / 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 ...Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase / 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
PYRIDOXAL-5'-PHOSPHATE / SUCCINYL-COENZYME A / 5-aminolevulinate synthase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsAstner, I. / Schulze, J.O. / van den Heuvel, J.J. / Jahn, D. / Schubert, W.-D. / Heinz, D.W.
CitationJournal: Embo J. / Year: 2005
Title: Crystal Structure of 5-Aminolevulinate Synthase, the First Enzyme of Heme Biosynthesis, and its Link to Xlsa in Humans.
Authors: Astner, I. / Schulze, J.O. / Van Den Heuvel, J.J. / Jahn, D. / Schubert, W.-D. / Heinz, D.W.
History
DepositionJul 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 23, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-AMINOLEVULINATE SYNTHASE
B: 5-AMINOLEVULINATE SYNTHASE
D: 5-AMINOLEVULINATE SYNTHASE
E: 5-AMINOLEVULINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,15512
Polymers174,6964
Non-polymers4,4598
Water1,982110
1
A: 5-AMINOLEVULINATE SYNTHASE
B: 5-AMINOLEVULINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5776
Polymers87,3482
Non-polymers2,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-57.2 kcal/mol
Surface area25770 Å2
MethodPISA
2
D: 5-AMINOLEVULINATE SYNTHASE
E: 5-AMINOLEVULINATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5776
Polymers87,3482
Non-polymers2,2294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-57.2 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.935, 91.356, 247.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41E
12B
22A
32D
42E
13D
23A
33B
43E
14E
24A
34B
44D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A3 - 320
2112B3 - 320
3112D3 - 320
4112E3 - 320
1212A328 - 338
2212B328 - 338
3212D328 - 338
4212E328 - 338
1316A339 - 356
2316B339 - 356
3316D339 - 356
4316E339 - 356
1412A357 - 380
2412B357 - 380
3412D357 - 380
4412E357 - 380
1512A381 - 399
2512B381 - 399
3512D381 - 399
4512E381 - 399
1122B3 - 320
2122A3 - 320
3122D3 - 320
4122E3 - 320
1222B328 - 338
2222A328 - 338
3222D328 - 338
4222E328 - 338
1326B339 - 356
2326A339 - 356
3326D339 - 356
4326E339 - 356
1422B357 - 380
2422A357 - 380
3422D357 - 380
4422E357 - 380
1526B381 - 399
2526A381 - 399
3526D381 - 399
4526E381 - 399
1132D3 - 320
2132A3 - 320
3132B3 - 320
4132E3 - 320
1232D328 - 338
2232A328 - 338
3232B328 - 338
4232E328 - 338
1336D339 - 356
2336A339 - 356
3336B339 - 356
4336E339 - 356
1432D357 - 380
2432A357 - 380
3432B357 - 380
4432E357 - 380
1536D381 - 399
2536A381 - 399
3536B381 - 399
4536E381 - 399
1142E3 - 320
2142A3 - 320
3142B3 - 320
4142D3 - 320
1242E328 - 338
2242A328 - 338
3242B328 - 338
4242D328 - 338
1346E339 - 356
2346A339 - 356
3346B339 - 356
4346D339 - 356
1442E357 - 380
2442A357 - 380
3442B357 - 380
4442D357 - 380
1546E381 - 399
2546A381 - 399
3546B381 - 399
4546D381 - 399

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
5-AMINOLEVULINATE SYNTHASE / 5-AMINOLEVULINIC ACID SYNTHASE / DELTA- AMINOLEVULINATE SYNTHASE / DELTA-ALA SYNTHETASE


Mass: 43673.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LYSINE 248 COVALENTLY BOUND TO PLP, CHAIN A / Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM 1710
Plasmid: PQE30 / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P18079, 5-aminolevulinate synthase
#2: Chemical
ChemComp-SCA / SUCCINYL-COENZYME A


Mass: 867.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H40N7O19P3S
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDIFFERENT STRAINS OF RHODOBACTER CAPSULATUS

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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: 2.21 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5
Details: 100 MM HEPES PH 7.5, 200 MM NA ACETATE, 8% (V/V) ISOPROPANOL, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2004 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 137995 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.8→119.52 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 26.87 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS MODELED WITH ZERO OCCUPANCY TO INDICATE THE PROBABLE LOCATION OF A CO-FACTOR IN THE ACTIVE STATE OF THE ENZYME.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1876 4.9 %RANDOM
Rwork0.16 ---
obs0.163 36616 99.3 %-
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: 26.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--1.55 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.8→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12209 0 283 110 12602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.97217200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05751589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91723.236550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04152030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7411590
X-RAY DIFFRACTIONr_chiral_restr0.1390.21868
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029661
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.26128
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.28706
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2451
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.55228075
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.688312605
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.49725177
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.08934595
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1476tight positional0.040.05
12B1476tight positional0.030.05
13D1476tight positional0.030.05
14E1476tight positional0.030.05
21B1408tight positional0.020.05
22A1408tight positional0.020.05
23D1408tight positional0.020.05
24E1408tight positional0.020.05
31D1408tight positional0.020.05
32A1408tight positional0.020.05
33B1408tight positional0.020.05
34E1408tight positional0.020.05
41E1408tight positional0.020.05
42A1408tight positional0.020.05
43B1408tight positional0.020.05
44D1408tight positional0.020.05
11A1356medium positional0.470.5
12B1356medium positional0.430.5
13D1356medium positional0.460.5
14E1356medium positional0.430.5
21B1284medium positional0.390.5
22A1284medium positional0.440.5
23D1284medium positional0.450.5
24E1284medium positional0.40.5
31D1284medium positional0.450.5
32A1284medium positional0.440.5
33B1284medium positional0.390.5
34E1284medium positional0.40.5
41E1284medium positional0.40.5
42A1284medium positional0.440.5
43B1284medium positional0.390.5
44D1284medium positional0.450.5
11A135loose positional0.375
12B135loose positional0.595
13D135loose positional0.385
14E135loose positional0.45
21B275loose positional0.625
22A275loose positional0.545
23D275loose positional0.425
24E275loose positional0.515
31D275loose positional0.425
32A275loose positional0.545
33B275loose positional0.625
34E275loose positional0.515
41E275loose positional0.515
42A275loose positional0.545
43B275loose positional0.625
44D275loose positional0.425
11A1476tight thermal0.040.5
12B1476tight thermal0.040.5
13D1476tight thermal0.040.5
14E1476tight thermal0.040.5
21B1408tight thermal0.040.5
22A1408tight thermal0.040.5
23D1408tight thermal0.040.5
24E1408tight thermal0.040.5
31D1408tight thermal0.040.5
32A1408tight thermal0.040.5
33B1408tight thermal0.040.5
34E1408tight thermal0.040.5
41E1408tight thermal0.040.5
42A1408tight thermal0.040.5
43B1408tight thermal0.040.5
44D1408tight thermal0.040.5
11A1356medium thermal0.482
12B1356medium thermal0.472
13D1356medium thermal0.512
14E1356medium thermal0.492
21B1284medium thermal0.442
22A1284medium thermal0.462
23D1284medium thermal0.482
24E1284medium thermal0.462
31D1284medium thermal0.482
32A1284medium thermal0.462
33B1284medium thermal0.442
34E1284medium thermal0.462
41E1284medium thermal0.462
42A1284medium thermal0.462
43B1284medium thermal0.442
44D1284medium thermal0.482
11A135loose thermal3.2710
12B135loose thermal2.9910
13D135loose thermal3.6310
14E135loose thermal3.110
21B275loose thermal2.1410
22A275loose thermal2.3310
23D275loose thermal2.5810
24E275loose thermal2.2110
31D275loose thermal2.5810
32A275loose thermal2.3310
33B275loose thermal2.1410
34E275loose thermal2.2110
41E275loose thermal2.2110
42A275loose thermal2.3310
43B275loose thermal2.1410
44D275loose thermal2.5810
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 136 -
Rwork0.26 2604 -
obs--96.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5-0.8254-0.5322.4218-1.45484.39670.1365-0.0246-0.1067-0.2703-0.0575-0.25970.2190.9204-0.079-0.0344-0.0220.04450.1886-0.0580.165542.5123.31117.369
21.0620.2538-0.37261.25271.00342.8390.13390.13480.1191-0.1823-0.0760.1582-0.3775-0.4734-0.05790.16480.0794-0.00710.16740.08850.22515.85311.57710.526
33.7623-1.4780.08111.97461.22313.59850.19540.3242-0.2295-0.36870.1553-0.1867-0.01150.5924-0.35070.0866-0.03030.05260.1485-0.04530.095738.0272.28-0.699
42.15051.0181-0.12083.07560.95412.01620.0479-0.14110.2993-0.3576-0.18420.442-0.8361-0.78040.13640.32120.20040.07950.19520.08240.31689.99228.62824.247
50.91970.2157-0.61571.8176-0.37772.57170.0669-0.09510.05440.15140.1133-0.0757-0.2190.2288-0.18020.109-0.01570.03020.1226-0.00090.196330.11210.83534.624
62.6555-1.22550.88322.63210.07362.2221-0.1409-0.16340.26870.43760.26480.0953-0.7754-0.203-0.12390.55210.08980.19230.0025-0.0280.126217.18132.80541.347
72.83851.0474-1.9282.4845-0.24773.15810.092-0.1294-0.26150.69780.0491-0.43560.25530.2251-0.14110.23430.0608-0.1021-0.0387-0.03580.141610.727-31.56751.451
80.70930.2810.27172.52520.11081.3164-0.07560.05340.06320.2351-0.06580.2181-0.1974-0.21980.14140.14880.02970.05520.0775-0.03120.1951-9.636-12.27744.969
93.48920.1441-0.77342.66450.20972.6979-0.0369-0.2240.04231.2826-0.0444-0.29990.18130.18620.08130.61770.0189-0.1128-0.10140.01770.03024.004-21.20265.558
100.7591-0.1490.26042.15040.69561.43410.01290.19960.1163-0.2792-0.27950.2049-0.1035-0.38270.2665-0.03330.0715-0.00810.2137-0.02910.2663-22.483-20.67228.419
110.8730.07960.00411.57070.3661.96930.06560.2408-0.00710.0127-0.008-0.08920.05430.1383-0.05760.10460.03410.03270.1096-0.03950.19264.211-30.9929.669
123.3723-0.15091.19630.08590.27942.46450.23370.41980.4041-0.239-0.29510.2317-0.081-0.2220.06150.07910.03960.01830.1843-0.0920.1944-18.134-33.76915.706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 52
2X-RAY DIFFRACTION2A53 - 296
3X-RAY DIFFRACTION3A297 - 397
4X-RAY DIFFRACTION4B1 - 52
5X-RAY DIFFRACTION5B53 - 296
6X-RAY DIFFRACTION6B297 - 397
7X-RAY DIFFRACTION7D1 - 52
8X-RAY DIFFRACTION8D53 - 296
9X-RAY DIFFRACTION9D297 - 397
10X-RAY DIFFRACTION10E1 - 52
11X-RAY DIFFRACTION11E53 - 296
12X-RAY DIFFRACTION12E297 - 398

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