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- PDB-4wji: Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizo... -

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Basic information

Entry
Database: PDB / ID: 4wji
TitleCrystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP and tyrosine
ComponentsPutative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase
KeywordsOXIDOREDUCTASE / Cyclohexadienyl dehydrogenase / NADP / tyrosine / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / nucleotide binding
Similarity search - Function
Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / TYROSINE / Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsShabalin, I.G. / Cooper, D.R. / Hou, J. / Zimmerman, M.D. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Hammonds, J. / Bonanno, J. / Seidel, R. ...Shabalin, I.G. / Cooper, D.R. / Hou, J. / Zimmerman, M.D. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Hammonds, J. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM094662 United States
CitationJournal: to be published
Title: Crystal structure of cyclohexadienyl dehydrogenase from Sinorhizobium meliloti in complex with NADP
Authors: Shabalin, I.G. / Cooper, D.R. / Hou, J. / Zimmerman, M.D. / Minor, W.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Data collection
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7418
Polymers31,6831
Non-polymers1,0577
Water4,954275
1
A: Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase
hetero molecules

A: Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,48116
Polymers63,3662
Non-polymers2,11514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12120 Å2
ΔGint-143 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.409, 68.891, 51.097
Angle α, β, γ (deg.)90.000, 94.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-543-

HOH

Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase


Mass: 31683.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: tyrC / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q92MG1, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor

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Non-polymers , 5 types, 282 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE PROTEIN WAS SUBJECTED TO LIMITED PROTEOLYSIS BY CHYMOTRYPSIN RIGHT BEFORE CRYSTALLIZATION. ...THE PROTEIN WAS SUBJECTED TO LIMITED PROTEOLYSIS BY CHYMOTRYPSIN RIGHT BEFORE CRYSTALLIZATION. SUPPOSINGLY THE HIS-TAG AND C-TERMINAL FRAGMENT WERE CLEAVED ON ONE OF THE POSSIBLE SITES. THE MAIN SUBSTRATES OF CHYMOTRYPSIN INCLUDE TRYPTOPHAN, TYROSINE, PHENYLALANINE, LEUCINE, AND METHIONINE, WHICH ARE CLEAVED AT THE CARBOXYL TERMINAL.

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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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azid, 0.5 mM TCEP, 7mM NADP and 20 mM tyrosine were mixed with 0.2 ul of the Index condition #83 (0.2 ...Details: 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azid, 0.5 mM TCEP, 7mM NADP and 20 mM tyrosine were mixed with 0.2 ul of the Index condition #83 (0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 49774 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.052 / Rrim(I) all: 0.084 / Χ2: 3.355 / Net I/av σ(I): 21.868 / Net I/σ(I): 14.3 / Num. measured all: 112812
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.421.70.3691.824210.7340.3360.5011.04193.4
1.42-1.451.90.33224890.7910.290.4421.07397.3
1.45-1.482.10.28425850.8620.2380.3721.15498.5
1.48-1.512.30.25525800.9070.2030.3271.28198.6
1.51-1.542.30.21925220.9220.1720.281.39898.4
1.54-1.582.30.19525520.9110.1540.2491.40698.2
1.58-1.622.30.1725470.9370.1340.2181.49798.2
1.62-1.662.30.15325570.9610.1190.1941.64897.9
1.66-1.712.30.13825160.9670.1060.1751.81897.6
1.71-1.762.40.12625400.9670.0970.162.15497.4
1.76-1.832.30.1125190.9740.0840.1392.55597
1.83-1.92.40.09725290.9810.0750.1233.11596.7
1.9-1.992.40.08724880.9840.0670.113.76696.3
1.99-2.092.30.07824820.9860.060.0994.65995.9
2.09-2.222.30.06824930.9880.0530.0874.78295.2
2.22-2.392.30.06924730.9830.0540.0886.18994.8
2.39-2.632.30.06524210.9840.0510.0836.37593.4
2.63-3.022.30.05724250.990.0440.0737.21291.9
3.02-3.82.40.04323560.9950.0330.0556.2790.3
3.8-502.40.04422790.9930.0340.0566.18484.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
DMphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.1537 / WRfactor Rwork: 0.1106 / FOM work R set: 0.8783 / SU B: 2.258 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0534 / SU Rfree: 0.0531 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1587 2524 5.1 %RANDOM
Rwork0.1151 47183 --
obs0.1173 49707 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.71 Å2 / Biso mean: 15.987 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-1.2 Å2
2---0.19 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 66 276 2504
Biso mean--12.47 32.48 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192291
X-RAY DIFFRACTIONr_bond_other_d0.0020.022173
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9813135
X-RAY DIFFRACTIONr_angle_other_deg1.63434977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8535300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79223.02386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01915332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7311516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212587
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02514
X-RAY DIFFRACTIONr_mcbond_it1.8021.2691182
X-RAY DIFFRACTIONr_mcbond_other1.8011181
X-RAY DIFFRACTIONr_mcangle_it2.2191.9081476
X-RAY DIFFRACTIONr_rigid_bond_restr4.81632287
X-RAY DIFFRACTIONr_sphericity_free20.1530.0185
X-RAY DIFFRACTIONr_sphericity_bonded11.4940.012432
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 186 -
Rwork0.239 3470 -
all-3656 -
obs--95.23 %

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