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- PDB-3jz4: Crystal structure of E. coli NADP dependent enzyme -

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Basic information

Entry
Database: PDB / ID: 3jz4
TitleCrystal structure of E. coli NADP dependent enzyme
ComponentsSuccinate-semialdehyde dehydrogenase [NADP+]
KeywordsOXIDOREDUCTASE / Tetramer / NADP binding / NADP
Function / homology
Function and homology information


glutarate-semialdehyde dehydrogenase (NADP+) activity / succinate-semialdehyde dehydrogenase (NADP+) / succinate-semialdehyde dehydrogenase (NADP+) activity / succinate-semialdehyde dehydrogenase [NAD(P)+] activity / succinate-semialdehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid catabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / : / NADP binding / protein homotetramerization
Similarity search - Function
Succinate semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Succinate semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Succinate-semialdehyde dehydrogenase [NADP(+)] GabD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLangendorf, C.G. / Key, T.L.G. / Fenalti, G. / Kan, W.T. / Buckle, A.M. / Caradoc-Davies, T. / Tuck, K.L. / Law, R.H.P. / Whisstock, J.C.
CitationJournal: Plos One / Year: 2010
Title: The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions.
Authors: Langendorf, C.G. / Key, T.L. / Fenalti, G. / Kan, W.T. / Buckle, A.M. / Caradoc-Davies, T. / Tuck, K.L. / Law, R.H. / Whisstock, J.C.
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
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_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: Succinate-semialdehyde dehydrogenase [NADP+]
B: Succinate-semialdehyde dehydrogenase [NADP+]
C: Succinate-semialdehyde dehydrogenase [NADP+]
D: Succinate-semialdehyde dehydrogenase [NADP+]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,6848
Polymers206,7114
Non-polymers2,9744
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21510 Å2
ΔGint-88 kcal/mol
Surface area56910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.885, 151.885, 165.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUARGARG1AA2 - 92 - 9
21LEULEUARGARG1BB2 - 92 - 9
31LEULEUARGARG1CC2 - 92 - 9
41LEULEUARGARG1DD2 - 92 - 9
12GLNGLNVALVAL1AA10 - 20810 - 208
22GLNGLNVALVAL1BB10 - 20810 - 208
32GLNGLNVALVAL1CC10 - 20810 - 208
42GLNGLNVALVAL1DD10 - 20810 - 208
13THRTHRALAALA6AA209 - 214209 - 214
23THRTHRALAALA6BB209 - 214209 - 214
33THRTHRALAALA6CC209 - 214209 - 214
43THRTHRALAALA6DD209 - 214209 - 214
14VALVALMETMET1AA215 - 312215 - 312
24VALVALMETMET1BB215 - 312215 - 312
34VALVALMETMET1CC215 - 312215 - 312
44VALVALMETMET1DD215 - 312215 - 312
15SERSERHISHIS6AA313 - 316313 - 316
25SERSERHISHIS6BB313 - 316313 - 316
35SERSERHISHIS6CC313 - 316313 - 316
45SERSERHISHIS6DD313 - 316313 - 316
16ILEILEPROPRO1AA317 - 329317 - 329
26ILEILEPROPRO1BB317 - 329317 - 329
36ILEILEPROPRO1CC317 - 329317 - 329
46ILEILEPROPRO1DD317 - 329317 - 329
17LEULEUALAALA4AA330 - 359330 - 359
27LEULEUALAALA4BB330 - 359330 - 359
37LEULEUALAALA4CC330 - 359330 - 359
47LEULEUALAALA4DD330 - 359330 - 359
18HISHISASNASN3AA360 - 365360 - 365
28HISHISASNASN3BB360 - 365360 - 365
38HISHISASNASN3CC360 - 365360 - 365
48HISHISASNASN3DD360 - 365360 - 365
19PHEPHEALAALA4AA366 - 400366 - 400
29PHEPHEALAALA4BB366 - 400366 - 400
39PHEPHEALAALA4CC366 - 400366 - 400
49PHEPHEALAALA4DD366 - 400366 - 400
110ASPASPGLUGLU1AA401 - 462401 - 462
210ASPASPGLUGLU1BB401 - 462401 - 462
310ASPASPGLUGLU1CC401 - 462401 - 462
410ASPASPGLUGLU1DD401 - 462401 - 462
111GLYGLYTYRTYR6AA463 - 466463 - 466
211GLYGLYTYRTYR6BB463 - 466463 - 466
311GLYGLYTYRTYR6CC463 - 466463 - 466
411GLYGLYTYRTYR6DD463 - 466463 - 466
112GLYGLYLEULEU1AA467 - 481467 - 481
212GLYGLYLEULEU1BB467 - 481467 - 481
312GLYGLYLEULEU1CC467 - 481467 - 481
412GLYGLYLEULEU1DD467 - 481467 - 481
DetailsFour monomers related by non-crystallographic 222 symetry

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Components

#1: Protein
Succinate-semialdehyde dehydrogenase [NADP+] / SSDH / NADP dependent enzyme


Mass: 51677.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC1061 / Gene: b2661, gabD, JW2636, NA / Plasmid: pRSETc / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P25526, succinate-semialdehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS SAID THEY BELIEVE THE MISMATCH OBSERVED REPRESENTS A NATURALLY OCCURRING VARIANT OF THE ...THE AUTHORS SAID THEY BELIEVE THE MISMATCH OBSERVED REPRESENTS A NATURALLY OCCURRING VARIANT OF THE E. COLI SSADH GENE. AUTHORS SEQUENCED MANY SSADH CDNA SEQUENCES FROM GENOMIC DNA ISOLATED FROM THE E. COLI VARIANT MC1061 AND FOUND THIS MISMATCH OCCURRED IN ALL SEQUENCES. THE MISMATCH ARISES FROM A SINGLE NUCLEOTIDE CHANGE FROM GTG TO ATG RESULTING IN A CHANGE IN THE PROTEIN SEQUENCE VAL TO MET.

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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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium tartrate, 30 % PEG 3350, 10 mM 2-mercaptoethanol, 0.1 M tris, pH 7.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 15, 2008 / Details: NA
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.3→37.56 Å / Num. obs: 74567 / Rmerge(I) obs: 0.188
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.56 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.169 / WRfactor Rwork: 0.135 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.878 / SU B: 13.053 / SU ML: 0.158 / SU R Cruickshank DPI: 0.518 / SU Rfree: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.518 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3717 5 %RANDOM
Rwork0.168 ---
obs0.17 74545 86.33 %-
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 max: 69.15 Å2 / Biso mean: 19.734 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14380 0 192 331 14903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02215060
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.97920475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05651977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03724.664639
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89152456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9361587
X-RAY DIFFRACTIONr_chiral_restr0.0940.22294
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211437
X-RAY DIFFRACTIONr_nbd_refined0.1980.27251
X-RAY DIFFRACTIONr_nbtor_refined0.30.210370
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2800
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.213
X-RAY DIFFRACTIONr_mcbond_it1.45649851
X-RAY DIFFRACTIONr_mcangle_it2.191615300
X-RAY DIFFRACTIONr_scbond_it1.84545862
X-RAY DIFFRACTIONr_scangle_it2.77565150
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2939TIGHT POSITIONAL0.060.05
B2939TIGHT POSITIONAL0.060.05
C2939TIGHT POSITIONAL0.040.05
D2939TIGHT POSITIONAL0.040.05
A467MEDIUM POSITIONAL0.60.5
B467MEDIUM POSITIONAL0.660.5
C467MEDIUM POSITIONAL0.390.5
D467MEDIUM POSITIONAL0.360.5
A107LOOSE POSITIONAL0.395
B107LOOSE POSITIONAL0.625
C107LOOSE POSITIONAL0.295
D107LOOSE POSITIONAL0.585
A2939TIGHT THERMAL0.110.5
B2939TIGHT THERMAL0.10.5
C2939TIGHT THERMAL0.090.5
D2939TIGHT THERMAL0.090.5
A467MEDIUM THERMAL0.742
B467MEDIUM THERMAL0.682
C467MEDIUM THERMAL0.662
D467MEDIUM THERMAL0.612
A107LOOSE THERMAL5.2710
B107LOOSE THERMAL2.610
C107LOOSE THERMAL2.9110
D107LOOSE THERMAL2.2410
LS refinement shellHighest resolution: 2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 246 -
Rwork0.17 4599 -
all-4845 -
obs-74567 77.17 %
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)
11.0855-0.59490.18261.3283-0.71051.33220.06280.14460.0794-0.1138-0.0783-0.1429-0.03580.16230.01550.0244-0.00240.0470.11920.00660.0769-6.66342.56959.8909
20.3491-0.0223-0.12540.27990.07170.24990.0194-0.00110.0186-0.0213-0.0026-0.0170.01730.0115-0.01680.05670.00940.00090.0788-0.01080.0674-18.853338.664622.3396
33.8948-0.1409-1.10660.9834-0.25921.92130.13950.35850.1655-0.1257-0.03850.0371-0.0567-0.1456-0.1010.04360.0277-0.00470.03450.03880.0473-37.759360.498311.5624
41.385-1.04860.28671.656-0.29460.5432-0.06470.03670.08050.07620.03460.0265-0.0008-0.05650.03010.055-0.02160.01970.07230.00190.0563-38.723742.086226.0531
51.2593-0.2880.19051.952-0.06761.14840.04520.0049-0.1307-0.242-0.02340.35570.0952-0.0684-0.02190.1118-0.0205-0.03270.0552-0.0030.0561-55.60119.584315.0519
60.38510.06130.12530.29420.05990.2940.0035-0.0197-0.0405-0.0304-0.0045-0.02650.0407-0.01770.0010.1031-0.0027-0.00180.06480.01410.0595-43.644718.485625.6486
71.74260.67770.34550.97770.54610.36450.02060.1816-0.3015-0.07910.0983-0.17390.05640.1003-0.11890.1390.02990.01120.0351-0.00870.1316-24.153-5.258623.1118
81.495-1.210.10191.88390.00710.4586-0.0251-0.0132-0.0840.04560.0935-0.12190.09310.0352-0.06840.082-0.0151-0.01390.06630.00740.0832-23.89816.930530.7837
90.5277-0.2171-0.78490.88750.0151.6996-0.08830.0027-0.04050.28030.02180.19420.2185-0.11430.06650.2186-0.03980.05250.09720.0070.0754-54.041118.558764.7875
100.26260.04320.01380.4780.03980.1848-0.0389-0.08130.01180.18960.01470.02620.0946-0.00630.02420.20580.0187-0.00040.14940.0150.0459-41.086626.811261.6239
110.47430.6774-0.88593.4833-1.40531.66250.06740.0780.02210.49450.07120.3743-0.1676-0.1545-0.13860.13660.02640.05980.14290.02990.1327-63.153949.589962.3528
121.073-0.7520.28691.4131-0.13840.7445-0.0153-0.130.00260.09030.01450.1286-0.1009-0.0940.00080.0947-0.01260.00780.10320.0020.0571-42.713844.067552.1067
134.2339-1.16650.53691.18230.44481.6091-0.146-0.1730.42340.14350.2569-0.3337-0.22130.2995-0.11090.1123-0.0055-0.06650.2113-0.13720.1907-9.622556.440667.4512
140.3196-0.03870.0250.43780.38720.6704-0.0376-0.15620.03240.08260.1231-0.10690.01410.1095-0.08550.10880.0254-0.03040.1772-0.05010.0842-19.050944.296757.0826
152.18140.43290.42924.25960.65551.1932-0.0313-0.69820.01780.46260.1466-0.070.25370.1558-0.11530.19140.1433-0.08350.3615-0.03550.0261-0.813521.818568.04
161.3702-0.6830.03541.2840.00590.8372-0.0525-0.2283-0.06340.21610.0911-0.12880.18510.155-0.03850.1490.0222-0.02690.1278-0.00140.0701-20.796623.610856.2609
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 60
2X-RAY DIFFRACTION2A61 - 264
3X-RAY DIFFRACTION3A265 - 394
4X-RAY DIFFRACTION4A395 - 481
5X-RAY DIFFRACTION5B1 - 58
6X-RAY DIFFRACTION6B59 - 264
7X-RAY DIFFRACTION7B265 - 394
8X-RAY DIFFRACTION8B395 - 481
9X-RAY DIFFRACTION9C1 - 113
10X-RAY DIFFRACTION10C114 - 264
11X-RAY DIFFRACTION11C265 - 394
12X-RAY DIFFRACTION12C395 - 481
13X-RAY DIFFRACTION13D1 - 58
14X-RAY DIFFRACTION14D59 - 264
15X-RAY DIFFRACTION15D265 - 394
16X-RAY DIFFRACTION16D395 - 481

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