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- PDB-4nmc: Crystal structure of oxidized proline utilization A (PutA) from G... -

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Basic information

Entry
Database: PDB / ID: 4nmc
TitleCrystal structure of oxidized proline utilization A (PutA) from Geobacter sulfurreducens PCA complexed with Zwittergent 3-12
ComponentsProline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / flavoenzyme / Rossmann fold / aldehyde dehydrogenase / flavin adenine dinucleotide / nicotinamide adenine dinucleotide / proline catabolism / substrate channeling / bifunctional enzyme
Function / homology
Function and homology information


proline dehydrogenase activity / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / L-glutamate gamma-semialdehyde dehydrogenase / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / cytoplasm
Similarity search - Function
Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Proline utilization A, N-terminal / Proline utilization A N-terminal domain / 1-pyrroline-5-carboxylate dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / FAD-linked oxidoreductase-like / 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
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / Chem-C15 / FLAVIN-ADENINE DINUCLEOTIDE / : / L-glutamate gamma-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsSingh, H. / Tanner, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of the PutA peripheral membrane flavoenzyme reveal a dynamic substrate-channeling tunnel and the quinone-binding site.
Authors: Singh, H. / Arentson, B.W. / Becker, D.F. / Tanner, J.J.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
B: Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,30811
Polymers224,6492
Non-polymers2,6599
Water20,2131122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-29 kcal/mol
Surface area65570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.078, 157.207, 190.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Proline dehydrogenase and Delta-1-pyrroline-5-carboxylate dehydrogenase / Proline utilization A / PutA


Mass: 112324.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: putA, GSU3395 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: Q746X3, EC: 1.5.99.8, EC: 1.5.1.12, L-glutamate gamma-semialdehyde dehydrogenase

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Non-polymers , 6 types, 1131 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H38NO3S
#6: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1122 / 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: 3.14 Å3/Da / Density % sol: 60.82 %
Crystal growTemperature: 298 K / Method: microbatch
Details: 0.10-0.25 M potassium sodium tartrate, 20-25% w/v PEG3350, MICROBATCH, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 7, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.1 % / Av σ(I) over netI: 7.1 / Number: 369061 / Rsym value: 0.105 / D res high: 2.568 Å / D res low: 121.065 Å / Num. obs: 90248 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.12121.0798.810.0230.0233.8
5.748.1299.810.0430.0434
4.695.7499.810.0490.0493.9
4.064.6999.810.0510.0514
3.634.0699.910.0690.0694.1
3.323.6399.910.0930.0934.1
3.073.3299.910.1540.1544.1
2.873.0799.910.2470.2474.2
2.712.8799.910.3350.3354.2
2.572.7199.210.4550.4554.1
ReflectionResolution: 1.891→47.039 Å / Num. all: 220275 / Num. obs: 220275 / % possible obs: 99.4 % / Redundancy: 5.3 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.109 / Rsym value: 0.098 / Net I/av σ(I): 6.511 / Net I/σ(I): 10.4 / Num. measured all: 1166275
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-24.30.6831.2134350310910.3660.7770.683296.9
2-2.1350.4681.7152511303610.2310.5230.4683.399.9
2.13-2.275.50.3172.5157284285520.1480.3510.3175.199.9
2.27-2.455.60.2243.5150463266370.1030.2480.2246.999.9
2.45-2.695.70.1584.9138851245600.0730.1750.1589.299.8
2.69-3.015.70.1166.5125899222480.0530.1280.11611.999.9
3.01-3.475.60.088.8109326196900.0370.0880.0817.799.6
3.47-4.255.30.05911.389109167090.0280.0660.05924.799.6
4.25-6.015.30.04912.969305130230.0230.0540.04926.899.6
6.01-47.0395.30.03516.73917774040.0160.0390.03527.499.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→47.039 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8695 / SU ML: 0.2 / σ(F): 0 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 11082 5.03 %RANDOM
Rwork0.1799 ---
obs0.1816 220154 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.06 Å2 / Biso mean: 31.0247 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: LAST / Resolution: 1.901→47.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14613 0 157 1122 15892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815122
X-RAY DIFFRACTIONf_angle_d1.04220522
X-RAY DIFFRACTIONf_chiral_restr0.0712251
X-RAY DIFFRACTIONf_plane_restr0.0052680
X-RAY DIFFRACTIONf_dihedral_angle_d14.8565529
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.901-1.9230.33083120.30386011632386
1.923-1.94560.29913670.280469527319100
1.9456-1.96940.28863550.262869357290100
1.9694-1.99430.28024120.256268897301100
1.9943-2.02050.2863540.248269437297100
2.0205-2.04820.26943340.229270127346100
2.0482-2.07750.27554010.236769047305100
2.0775-2.10850.27323540.220569537307100
2.1085-2.14140.23093910.204869517342100
2.1414-2.17660.25934060.205969257331100
2.1766-2.21410.23633950.192969477342100
2.2141-2.25430.23523380.19669457283100
2.2543-2.29770.21963860.187269867372100
2.2977-2.34460.20923740.181469687342100
2.3446-2.39560.21123560.174869557311100
2.3956-2.45130.20963700.174170237393100
2.4513-2.51260.21473970.174269057302100
2.5126-2.58050.23453680.175970297397100
2.5805-2.65650.22013680.176169807348100
2.6565-2.74220.22723730.17769637336100
2.7422-2.84020.20953470.174770327379100
2.8402-2.95390.20653440.180370677411100
2.9539-3.08830.22243630.187369957358100
3.0883-3.25110.22963970.190170057402100
3.2511-3.45470.19273650.17027013737899
3.4547-3.72140.17823650.157870677432100
3.7214-4.09570.19073740.148670657439100
4.0957-4.68790.16753610.139171077468100
4.6879-5.90440.183830.154471617544100
5.9044-47.05340.2023720.18087384775699

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