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- PDB-5bnt: X-ray Crystal Structure of a Aspartate-semialdehyde dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 5bnt
TitleX-ray Crystal Structure of a Aspartate-semialdehyde dehydrogenase bound to NADP from Pseudomonas aeruginosa
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Pseudomonas aeruginosa / aspartate-semialdehyde dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / L-threonine biosynthetic process / : / : / : / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: X-ray Crystal Structure of a Aspartate-semialdehyde dehydrogenase bound to NADP from Pseudomonas aeruginosa
Authors: Fairman, J.W. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
A: Aspartate-semialdehyde dehydrogenase
D: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,2528
Polymers166,2794
Non-polymers2,9744
Water16,718928
1
C: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6264
Polymers83,1392
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-41 kcal/mol
Surface area26730 Å2
MethodPISA
2
A: Aspartate-semialdehyde dehydrogenase
D: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6264
Polymers83,1392
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-44 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.680, 125.680, 199.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Aspartate-semialdehyde dehydrogenase / ASADH / Aspartate-beta-semialdehyde dehydrogenase


Mass: 41569.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: asd, PA3117 / Plasmid: PsaeA.17885.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q51344, aspartate-semialdehyde dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 928 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytics, MCSG1 D9: 0.2 M sodium chloride, 0.1 M TRIS:HCl pH 8.50, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 90696 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 7.58 % / Biso Wilson estimate: 19.55 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.133 / Χ2: 0.941 / Net I/σ(I): 15.13 / Num. measured all: 688175
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.150.8410.5723.5950949680666440.60997.6
2.15-2.210.890.4924.249756666865010.52497.5
2.21-2.280.9170.4135.1147003646562910.4497.3
2.28-2.350.9440.3655.7146762629661610.38897.9
2.35-2.420.960.3036.845260613059800.32397.6
2.42-2.510.9640.2867.3543405589157520.30497.6
2.51-2.60.9740.258.4142161570555980.26698.1
2.6-2.710.9790.2239.4540599551953760.23897.4
2.71-2.830.9850.18410.9738886529251580.19697.5
2.83-2.970.990.14913.3237487507949450.15897.4
2.97-3.130.9930.12715.435693481646890.13597.4
3.13-3.320.9950.09918.6934138459544480.10696.8
3.32-3.550.9970.07424.1731753430441500.07996.4
3.55-3.830.9980.06427.9229594403538880.06896.4
3.83-4.20.9990.04933.6327256374235790.05395.6
4.2-4.70.9990.03939.6324945339132320.04295.3
4.7-5.420.9990.03939.2722000301528670.04295.1
5.42-6.640.9990.04235.8518679259324450.04494.3
6.64-9.390.9990.03343.714327204518920.03592.5
9.390.9990.02649.787522123711000.02888.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(dev_2050: ???)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MB4

1mb4


Resolution: 2.1→43.484 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 2000 2.21 %RANDOM
Rwork0.1806 88603 --
obs0.1815 90603 96.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.55 Å2 / Biso mean: 24.2562 Å2 / Biso min: 6.62 Å2
Refinement stepCycle: final / Resolution: 2.1→43.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11169 0 157 928 12254
Biso mean--40.36 29.27 -
Num. residues----1481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211605
X-RAY DIFFRACTIONf_angle_d0.75915812
X-RAY DIFFRACTIONf_chiral_restr0.0351801
X-RAY DIFFRACTIONf_plane_restr0.0042040
X-RAY DIFFRACTIONf_dihedral_angle_d15.6536973
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 (%)
2.1-2.15250.30431420.23046278642098
2.1525-2.21070.2711420.21426280642297
2.2107-2.27580.2511410.2086273641497
2.2758-2.34920.241420.19796280642298
2.3492-2.43320.21751420.19466331647398
2.4332-2.53060.24051430.19386315645898
2.5306-2.64580.24111430.1976339648298
2.6458-2.78520.24561430.19936327647097
2.7852-2.95970.23631430.19286319646297
2.9597-3.18820.22161430.19146353649697
3.1882-3.50890.22681430.17676335647897
3.5089-4.01630.17371430.16146334647796
4.0163-5.05890.18681440.13826358650295
5.0589-43.4930.19781460.1656481662793
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)
11.1501-0.5222-0.77790.7809-0.21491.42080.2794-0.17460.54440.45860.13430.1124-0.725-0.1064-0.17990.5680.09050.2520.3386-0.03160.4486-112.150239.253241.5008
21.7315-0.7105-1.51711.1673-0.26792.5837-0.0234-0.11660.02560.31810.10170.2755-0.0413-0.186-0.10020.2203-0.00390.09070.25840.00850.2446-111.348322.091940.1429
31.42940.3245-0.21131.11280.02651.13390.0453-0.11010.17280.0859-0.04480.0065-0.13310.02220.01430.12680.0167-0.0040.1136-0.01290.1083-88.442828.140227.5995
41.155-0.3531-0.41570.971-0.19211.09450.05380.11730.0661-0.0643-0.04520.203-0.0213-0.2249-0.00980.10810.0243-0.00010.17460.01540.1577-101.876123.753718.7721
56.14620.2981-0.61312.13980.09290.54070.09850.2270.5987-0.15520.25570.0556-0.29660.3224-0.28590.2084-0.0760.02240.378-0.0160.2985-4.510126.318215.0749
62.6291-0.56590.0261.60090.12755.4639-0.39990.85120.4726-0.62610.4078-0.1687-0.70570.3643-0.01480.4902-0.21370.01190.64070.11190.3934-3.275225.96561.0713
70.49551.22610.33023.0340.81780.2212-0.23890.66240.0088-0.77130.26450.1155-0.0841-0.087-0.0070.2651-0.0877-0.01640.5932-0.07440.1913-9.568613.79782.5395
82.10960.8753-1.0761.32971.30873.7331-0.13330.2859-0.52780.13260.0525-0.09210.44320.11240.05950.14380.0235-0.01010.2851-0.06390.2102-11.3857.81616.6656
91.0972-0.16190.11831.6257-0.42721.08540.0988-0.00690.2315-0.1575-0.0604-0.0916-0.14060.1358-0.03450.15-0.03870.03780.1193-0.030.1316-30.241626.339726.9876
101.0495-1.2567-0.86423.52841.11851.87040.16850.17790.0892-0.1635-0.18970.1218-0.2468-0.09270.03090.1182-0.0049-0.00980.1519-0.01880.1139-38.836727.802518.7641
114.3214-0.1748-0.14152.27470.01963.88230.04690.2778-0.1691-0.0298-0.0578-0.25210.19270.50510.02830.14650.01080.00320.1508-0.06170.1188-22.73273.828319.3413
121.42230.15190.23570.0513-0.01311.31770.05930.0370.0801-0.0072-0.0033-0.12320.08450.2185-0.03980.0868-0.00510.030.153-0.01950.1261-27.12616.529426.2935
131.22440.0846-0.2011.27050.21181.28550.0237-0.1433-0.01570.097-0.0132-0.06130.1020.3359-0.01810.11030.0111-0.01710.1805-0.0260.0895-20.207913.477338.9602
141.5661.644-0.97263.1091-0.33713.64510.19450.19810.046-0.1446-0.00070.0204-0.08130.234-0.19260.1055-0.0237-0.00190.2525-0.04120.1299-7.926318.651817.1556
150.8018-0.3928-0.56231.65960.79651.76460.0028-0.05390.02370.05430.00970.022-0.05620.07-0.01120.0687-0.03030.01760.1372-0.00210.1123-57.635927.477548.9105
161.1445-0.1003-0.11190.90940.20760.96110.096-0.04630.06750.0132-0.0545-0.0637-0.04260.07970.00650.0998-0.02340.02060.1082-0.02690.0902-36.869920.963632.4688
170.8661-0.6485-0.53810.5980.34291.26580.03320.0157-0.0533-0.046-0.03890.0598-0.014-0.03580.00220.0859-0.04220.00590.0794-0.02050.1096-49.384319.02733.5119
182.5422-0.0042-1.08053.109-1.07612.83930.1711-0.26280.21870.1407-0.00480.0215-0.50910.0428-0.15540.2191-0.00380.04050.1841-0.03880.1375-57.706735.73167.6948
191.74090.6463-1.05193.49580.37043.18110.14150.16870.1652-0.2462-0.0975-0.0299-0.2235-0.1204-0.0360.16660.04650.03150.13310.00650.1104-59.879733.5131-4.3249
200.98820.7585-1.20882.478-1.4262.9043-0.14430.198-0.1175-0.1980.09620.00350.025-0.44890.05290.1420.03870.02440.21630.01530.1459-64.92519.8849-1.5402
213.76140.2585-2.57142.07840.14625.80370.0229-0.0275-0.0648-0.1025-0.026-0.1387-0.1086-0.0561-0.02550.14560.02540.00060.1295-0.02580.1112-66.547616.46485.3619
221.4953-0.44640.04171.8856-0.2321.10960.0508-0.05250.2655-0.0678-0.04980.0549-0.22740.083-0.03160.1271-0.0130.01210.1151-0.00560.127-84.655131.975420.3921
231.869-0.41950.06751.72460.28382.20280.09690.29410.398-0.2147-0.01580.0721-0.3025-0.00770.00530.21160.03380.02040.16890.08170.2354-92.403238.092113.3502
247.3090.2375-1.04972.788-0.79983.7325-0.02020.45460.0793-0.3801-0.00490.11240.07840.1880.04010.2251-0.01620.00780.2315-0.03130.081-79.547614.09165.006
252.32170.65880.71321.66520.46760.8375-0.08440.11060.1663-0.0790.00150.073-0.04420.11340.08960.12540.01890.01410.15720.01790.1004-82.588823.067416.1375
263.01350.9940.23431.8716-0.26931.97770.1959-0.3294-0.30320.1916-0.134-0.05110.16110.2553-0.09010.21740.08060.03250.16750.04940.1475-73.11838.086624.589
270.94850.7189-1.55182.1056-1.37952.79070.0952-0.26960.09140.0824-0.1915-0.1667-0.05540.38510.06710.102-0.0111-0.02270.1759-0.03110.1287-75.368123.469729.7284
282.30461.4918-1.68771.1033-0.76522.11910.0635-0.0855-0.0444-0.0052-0.0357-0.0306-0.07590.1641-0.04460.12010.0374-0.01670.14970.00490.1058-71.32120.083415.5377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 62 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 142 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 260 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 261 through 378 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 31 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 67 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 95 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 142 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 143 through 199 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 200 through 237 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 238 through 260 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 261 through 281 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 282 through 349 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 350 through 378 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 10 through 142 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 143 through 317 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 318 through 378 )C0
18X-RAY DIFFRACTION18chain 'D' and (resid 8 through 47 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 48 through 82 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 83 through 119 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 120 through 142 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 143 through 199 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 200 through 236 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 237 through 260 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 261 through 281 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 282 through 305 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 306 through 330 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 331 through 378 )D0

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