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- PDB-3ktd: CRYSTAL STRUCTURE OF A PUTATIVE PREPHENATE DEHYDROGENASE (CGL0226... -

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Basic information

Entry
Database: PDB / ID: 3ktd
TitleCRYSTAL STRUCTURE OF A PUTATIVE PREPHENATE DEHYDROGENASE (CGL0226) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 AT 2.60 A RESOLUTION
ComponentsPrephenate dehydrogenase
KeywordsOXIDOREDUCTASE / PREPHENATE DEHYDROGENAS / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process
Similarity search - Function
6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle ...6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Prephenate dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Prephenate dehydrogenase (NP_599479.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_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_comp_id / _struct_conn.ptnr2_label_seq_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: Prephenate dehydrogenase
B: Prephenate dehydrogenase
C: Prephenate dehydrogenase
D: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0456
Polymers146,8774
Non-polymers1682
Water1,65792
1
A: Prephenate dehydrogenase
B: Prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6074
Polymers73,4392
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7910 Å2
ΔGint-63 kcal/mol
Surface area24130 Å2
MethodPISA
2
C: Prephenate dehydrogenase
D: Prephenate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)73,4392
Polymers73,4392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-61 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.322, 107.230, 146.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A5 - 340
2116B5 - 340
3116C5 - 340
4116D5 - 340
DetailsCRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein
Prephenate dehydrogenase /


Mass: 36719.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: Cgl0226 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8NTS6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 10.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M citric acid pH 4.0, Additive: 0.001 M Nicotinamide-adenine-dinucleotide (NAD), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97947,0.97883
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979471
30.978831
ReflectionResolution: 2.6→29.527 Å / Num. obs: 48978 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 58.039 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.674.20.7751.91495735640.775100
2.67-2.744.20.6251.21454934640.625100
2.74-2.824.20.5431.41424534040.543100
2.82-2.914.20.461.61387033080.46100
2.91-34.20.3572.11342932060.357100
3-3.114.20.3032.51292930870.303100
3.11-3.224.20.2343.31252529970.234100
3.22-3.364.20.1724.41203928770.172100
3.36-3.514.20.1355.51154127620.135100
3.51-3.684.20.1056.91113626650.105100
3.68-3.884.20.0917.91048325230.091100
3.88-4.114.10.0788.8995523990.078100
4.11-4.394.10.06610.1926322480.066100
4.39-4.754.10.05511.8873321370.055100
4.75-5.24.10.05811.5802719590.058100
5.2-5.814.10.06510.4720817670.065100
5.81-6.7140.06310.6642015880.063100
6.71-8.2240.04912.6538413570.049100
8.22-11.633.80.04111.9408910680.041100
11.63-29.533.50.0459.520935980.04594.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.6→29.527 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 29.158 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.613 / ESU R Free: 0.305
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.A PEG6000 FRAGMENT (PEG) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.RAMACHANDRAN OUTLIER AT RESIDUE A294 IS IN A REGION OF POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2475 5.1 %RANDOM
Rwork0.213 ---
obs0.215 48915 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.85 Å2 / Biso mean: 38.93 Å2 / Biso min: 4.15 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å20 Å20 Å2
2---0.79 Å20 Å2
3----3.89 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9443 0 11 92 9546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0219681
X-RAY DIFFRACTIONr_bond_other_d0.0010.026179
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.94313208
X-RAY DIFFRACTIONr_angle_other_deg0.956315065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.551283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.623.492398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.412151435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.081568
X-RAY DIFFRACTIONr_chiral_restr0.0680.21550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021938
X-RAY DIFFRACTIONr_mcbond_it0.56126364
X-RAY DIFFRACTIONr_mcbond_other0.07722623
X-RAY DIFFRACTIONr_mcangle_it1.146410132
X-RAY DIFFRACTIONr_scbond_it2.0363317
X-RAY DIFFRACTIONr_scangle_it3.17383070
Refine LS restraints NCS

Ens-ID: 1 / Number: 3696 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.495
2BLOOSE POSITIONAL0.485
3CLOOSE POSITIONAL0.55
4DLOOSE POSITIONAL0.545
1ALOOSE THERMAL2.7810
2BLOOSE THERMAL1.8810
3CLOOSE THERMAL2.9310
4DLOOSE THERMAL2.2110
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 199 -
Rwork0.31 3353 -
all-3552 -
obs--99.86 %
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)
12.70280.785-0.50710.61030.11840.7135-0.17950.0120.0659-0.10530.00920.07020.0783-0.08990.17030.0403-0.0311-0.00430.05730.00780.13299.369293.183636.7337
22.40150.82070.48872.0187-0.12481.9429-0.022-0.25360.08270.289-0.0922-0.2574-0.65830.36040.11420.2591-0.1218-0.05220.18920.0360.091945.1936111.372938.3181
33.0426-1.93941.96632.9789-1.97552.6191-0.18520.0690.30060.2458-0.01280.083-0.7083-0.11960.1980.29650.0653-0.05050.0593-0.02990.13819.0645117.096172.4659
42.1431-1.097-0.00530.8503-0.57751.8069-0.0030.21230.0716-0.0238-0.2048-0.14110.11450.50390.20780.04130.0468-0.05760.20.01840.174341.896394.022177.5922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 340
2X-RAY DIFFRACTION2B5 - 340
3X-RAY DIFFRACTION3C5 - 340
4X-RAY DIFFRACTION4D5 - 340

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