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- PDB-2gpe: Structure of the DNA-binding domain of E. Coli Proline Utilizatio... -

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Basic information

Entry
Database: PDB / ID: 2gpe
TitleStructure of the DNA-binding domain of E. Coli Proline Utilization A (PUTA)
ComponentsBifunctional protein putA
KeywordsDNA BINDING PROTEIN / PUTA / RIBBON-HELIX-HELIX / DNA-BINDING DOMAIN / PROLINE CATABOLISM / PROLINE UTILIZATION A
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding ...proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding / response to oxidative stress / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / PutA, RHH domain / Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Met repressor-like ...: / PutA, RHH domain / Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Met repressor-like / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / Arc Repressor Mutant / FAD-linked oxidoreductase-like / Arc-type ribbon-helix-helix / Ribbon-helix-helix / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / Bifunctional protein PutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJenkins, J.L. / Larson, J. / Tanner, J.J.
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structures of the DNA-binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys9 in DNA recognition.
Authors: Larson, J.D. / Jenkins, J.L. / Schuermann, J.P. / Zhou, Y. / Becker, D.F. / Tanner, J.J.
History
DepositionApr 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Bifunctional protein putA
B: Bifunctional protein putA
C: Bifunctional protein putA
D: Bifunctional protein putA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1078
Polymers23,8314
Non-polymers2764
Water1,22568
1
A: Bifunctional protein putA
B: Bifunctional protein putA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0544
Polymers11,9152
Non-polymers1382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-26 kcal/mol
Surface area6050 Å2
MethodPISA
2
C: Bifunctional protein putA
D: Bifunctional protein putA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0544
Polymers11,9152
Non-polymers1382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.731, 55.731, 125.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dimer. There are two dimers in the asymmetric unit with chain labels A/B and C/D.

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Components

#1: Protein
Bifunctional protein putA


Mass: 5957.746 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: putA / Plasmid: pKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P09546
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M AMMONIUM SULFATE, 0.05M BIS-TRIS, 30% PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH). N-TERMINAL HIS TAG REMOVED BY TREATMENT WITH TEV PROTEASE , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.2398 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.9→50.9 Å / Num. obs: 16253 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.03 % / Biso Wilson estimate: 32.313 Å2 / Rmerge(I) obs: 0.043 / Χ2: 0.98 / Net I/σ(I): 25.5 / Scaling rejects: 1601
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 98 % / Redundancy: 8.29 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.7 / Num. measured all: 13007 / Num. unique obs: 1549 / Χ2: 1.58

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å25.45 Å
Translation2.5 Å25.45 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4LDzdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AY0

2ay0


Resolution: 1.9→50.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.216 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 815 5 %RANDOM
Rwork0.203 ---
all0.205 ---
obs-16185 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 20 68 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221539
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9622084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3255195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.13622.92365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37215275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.311515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021131
X-RAY DIFFRACTIONr_nbd_refined0.1980.2677
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21052
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.211
X-RAY DIFFRACTIONr_mcbond_it0.3921.5989
X-RAY DIFFRACTIONr_mcangle_it0.56221536
X-RAY DIFFRACTIONr_scbond_it1.0693637
X-RAY DIFFRACTIONr_scangle_it1.6414.5543
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 59 -
Rwork0.257 1067 -
obs-1126 97.32 %
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)
117.8442-30.6666-1.3821105.767127.757512.24820.5234-0.8771-0.10240.3178-0.16740.68830.5229-0.9262-0.3560.4081-0.29910.11890.22310.13430.1766-35.6684-8.6151-1.3028
216.751926.2893-18.676995.2436-71.659254.0428-0.1151-0.5455-1.18890.34860.1079-2.1538-1.1824-0.11710.00720.07270.13210.1132-0.09680.07560.1788-32.03456.8072-1.0765
30.9786-5.4144-4.113447.70683.813337.5086-0.45880.3690.04860.2502-0.2622.5342-0.8169-1.74680.72080.03660.0269-0.0533-0.11890.01280.1367-30.795911.111-6.0691
44.5919-2.7987-6.542926.33826.62589.6053-0.44770.4630.2838-0.37410.08250.5862-0.4834-0.14070.36520.0224-0.0463-0.0612-0.19480.0349-0.0914-27.33828.9006-9.8272
58.69213.1861.831322.353631.33544.7676-0.31731.640.1576-0.2588-0.3897-0.1167-1.58840.24720.70710.083-0.09160.0151-0.08110.0813-0.1474-24.64525.8994-15.3724
67.08312.67581.50114.17165.722119.6492-0.61840.36150.5987-0.70390.694-0.7687-0.16771.133-0.0756-0.0241-0.0428-0.0163-0.12150.0044-0.1211-24.30581.204-16.2834
717.6804-9.948312.309815.6357-3.214921.0739-0.10520.2079-0.4633-0.41550.27470.63250.7051-0.0588-0.1694-0.0431-0.03460.0179-0.2003-0.0086-0.209-26.8863-3.1439-9.2783
817.0201-11.39579.746318.18-13.712810.47740.45180.1539-0.2432-1.1743-0.2154-0.56811.2470.2138-0.23640.00080.00760.0502-0.1418-0.0363-0.2111-22.4228-5.6443-5.0718
913.72352.91567.895815.1235-9.554713.24120.0064-0.3446-0.358-0.49910.0012-0.83120.70110.7602-0.0076-0.12850.04360.0321-0.0802-0.0233-0.1196-18.0029-6.0093-0.1064
1035.9633-2.8266.468922.2747-2.630413.3424-1.2844-0.97420.81971.33290.8464-1.8622-0.82910.12190.4380.09740.1288-0.10370.0633-0.05860.1363-12.6559-8.21454.4365
1113.0869-1.5696-3.4799101.33122.6445.80981.57630.47610.5446-3.1308-2.09441.9099-1.1767-1.4710.51810.28750.146-0.14380.1460.12320.4422-35.69044.5108-2.8971
1226.9297-14.548318.693429.19-27.276826.81-1.10251.16280.547-0.35120.74390.48310.0068-0.16930.35860.0463-0.104-0.0924-0.14980.029-0.0153-31.5394-11.6884-2.2774
135.88691.71262.747338.436622.504252.4332-0.39190.0271-0.09410.2632-0.41582.12530.9186-1.2280.8076-0.0824-0.01950.0337-0.1690.0231-0.0602-29.285-12.45762.9075
149.02425.0856-0.475521.6777-4.232519.49870.1306-0.5238-0.477-0.383-0.1066-0.2690.31940.6392-0.0241-0.17750.03260.0125-0.17020.0369-0.1811-25.4946-9.94085.6332
1518.214819.383917.367323.339414.540825.47540.2733-1.0538-0.70950.3493-0.0296-0.9480.82670.0589-0.2437-0.20930.0066-0.0013-0.02020.0437-0.1117-21.5843-6.264111.6948
164.4057-2.3339-1.078818.00966.864711.5228-0.1562-0.7572-0.25440.28220.183-0.2789-0.4241-0.5468-0.0268-0.1813-0.0413-0.0113-0.01830.0076-0.2173-25.4851-0.773911.0765
1716.825812.7361-12.10512.2031-2.417226.46410.0384-0.68430.5781-0.17710.07910.5044-0.7097-0.1208-0.1174-0.18480.0556-0.0231-0.1168-0.0356-0.1759-26.2781.48754.2941
1811.312910.9284-8.493416.6191-10.423620.3033-0.1862-0.1320.56920.3545-0.0868-0.2998-0.64790.90910.273-0.137-0.0384-0.0227-0.1299-0.0246-0.1509-21.49553.7304-0.5577
1939.201111.2842-5.686634.9199-2.578724.2819-0.3610.3373-0.3421-0.10960.2544-3.0449-0.91271.79310.1066-0.0078-0.10350.06590.0534-0.00270.022-17.31234.1466-6.3219
2035.9811-14.1218.541223.48155.63816.5328-0.26260.99761.498-2.23710.768-1.715-1.07922.4008-0.50540.1574-0.19550.16620.51850.1580.1739-15.6397.7757-10.7464
213.742113.01290.5603125.994124.59726.4370.90050.06760.4924-1.52690.09820.8325-0.6129-1.2526-0.99870.43730.4017-0.17-0.04490.21370.2135-36.2159-18.6484-15.8287
2222.615-26.64566.8472123.5587-31.755729.64380.05321.14050.0317-2.12641.1301-0.05831.2485-0.3886-1.1833-0.0312-0.0886-0.122-0.05870.0803-0.0488-32.634-33.8639-17.9935
2317.04291.937719.586112.750315.60741.5810.2222-0.7116-0.78950.2942-0.1421.13581.0948-1.4275-0.08020.0148-0.0403-0.1263-0.18460.06580.0129-30.6732-38.0253-12.2748
247.83573.869711.035517.799810.87718.41620.3429-0.2631-0.5003-0.1949-0.1830.24530.70540.0029-0.1598-0.09580.0371-0.0658-0.22860.0388-0.1239-25.8324-35.1115-7.5339
2522.0893-0.16857.547150.82.281317.7105-0.3172-0.2695-0.78020.45040.6937-1.59870.60250.6802-0.3765-0.23030.0041-0.0378-0.07370.0489-0.1914-20.9514-30.9244-1.0118
2612.28914.47554.310513.665-4.739424.28280.24690.12670.15030.0412-0.16620.4151-0.85630.1064-0.0807-0.15950.012-0.0109-0.20530.0183-0.1971-26.4837-24.8158-5.2752
2716.1168.8435-3.625721.174-15.892825.4075-0.0264-0.0820.10220.6142-0.0457-0.1739-0.76320.4620.072-0.13530.0171-0.0639-0.1962-0.0081-0.2558-24.773-23.9583-10.6963
2818.31648.85955.881115.1965-5.378513.29110.0209-0.1650.56690.5525-0.0434-0.0756-0.53270.14140.0225-0.09020.0012-0.0217-0.14870.0107-0.2113-22.0809-21.2016-15.0083
2923.76656.7056-1.855929.7225-9.000234.0007-0.12270.8478-0.26390.09450.192-2.30320.25761.776-0.0693-0.0672-0.0390.0413-0.0042-0.0118-0.0532-17.9015-21.1025-19.9375
3071.73286.0425-2.06258.7787-9.11139.71870.00030.91551.4516-1.6894-0.7026-2.67090.40252.640.70230.30930.12060.08770.36330.17420.1626-16.0149-17.3237-24.3328
3113.482327.22558.9472164.184624.06366.26691.2416-0.6018-1.13162.2689-1.3987-1.26090.2443-1.33170.15710.25380.03540.13310.06890.1580.2061-35.4757-32.048-14.7715
329.96319.5985-7.7654.7255-42.267432.65980.8699-1.27550.56490.7861-0.12920.7124-0.94340.381-0.74070.19850.09160.0812-0.12360.0042-0.0381-32.2163-15.6033-15.0495
3316.2067-9.67141.49132.5529-4.376158.441-0.10150.3458-0.18060.2046-0.07471.40150.0351-0.69430.1762-0.03130.0782-0.001-0.18150.0074-0.1241-29.7502-14.3054-20.494
3413.9561-1.758-3.616510.96756.559920.9859-0.310.67680.609-0.19350.00890.22-1.1513-0.10060.3012-0.01270.022-0.0874-0.13290.015-0.1827-26.1975-17.2073-24.4735
353.75124.99617.482424.8123-4.713726.7916-0.61350.6833-0.1704-0.16520.9461-0.7737-1.05140.4688-0.33260.01240.0034-0.00020.112-0.0648-0.1937-23.7824-21.1775-31.9331
3616.9871-2.68460.017315.2106-4.800623.25490.20120.7813-0.4072-0.52170.0814-0.00770.53170.5571-0.2826-0.06220.004-0.087-0.0664-0.0682-0.2423-27.8682-26.8852-26.6714
3715.707-4.383511.6423.684-9.221932.65970.14510.5923-0.5666-0.12960.0909-0.0750.42580.1803-0.236-0.09160.0053-0.0295-0.2042-0.0293-0.1705-25.0646-28.1714-20.1459
3823.97063.02084.621413.955-8.257916.8597-0.17450.4054-0.206-0.03010.0451-0.2939-0.03190.52450.1293-0.10790.0513-0.0591-0.1362-0.0639-0.1543-20.4078-31.0507-15.0595
3939.486914.705312.432628.33872.228947.4397-0.09950.8834-0.4079-0.7962-0.1697-0.50850.51980.57810.2692-0.12460.0869-0.0522-0.0973-0.040.0081-15.951-33.0916-12.3789
40328.1553-6.489953.7609283.7334-53.646818.55710.27860.7961-3.1384-5.19960.3239-1.7558-0.8511-3.7477-0.60240.27610.1523-0.22110.6602-0.41610.4332-8.0154-35.4775-10.6538
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 72 - 7
22AA8 - 118 - 11
33AA12 - 1512 - 15
44AA16 - 1916 - 19
55AA20 - 2320 - 23
66AA24 - 2924 - 29
77AA30 - 3430 - 34
88AA35 - 3835 - 38
99AA39 - 4239 - 42
1010AA43 - 4843 - 48
1111BB2 - 82 - 8
1212BB9 - 129 - 12
1313BB13 - 1613 - 16
1414BB17 - 2017 - 20
1515BB21 - 2521 - 25
1616BB26 - 2926 - 29
1717BB30 - 3430 - 34
1818BB35 - 3935 - 39
1919BB40 - 4340 - 43
2020BB44 - 4744 - 47
2121CC2 - 72 - 7
2222CC8 - 118 - 11
2323CC12 - 1512 - 15
2424CC16 - 2216 - 22
2525CC23 - 2623 - 26
2626CC27 - 3127 - 31
2727CC32 - 3532 - 35
2828CC36 - 3936 - 39
2929CC40 - 4340 - 43
3030CC44 - 4744 - 47
3131DD2 - 82 - 8
3232DD9 - 129 - 12
3333DD13 - 1613 - 16
3434DD17 - 2217 - 22
3535DD23 - 2623 - 26
3636DD27 - 3127 - 31
3737DD32 - 3732 - 37
3838DD38 - 4138 - 41
3939DD42 - 4542 - 45
4040DD46 - 4946 - 49

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