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- PDB-4k28: 2.15 Angstrom resolution crystal structure of a shikimate dehydro... -

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Basic information

Entry
Database: PDB / ID: 4k28
Title2.15 Angstrom resolution crystal structure of a shikimate dehydrogenase family protein from Pseudomonas putida KT2440 in complex with NAD+
ComponentsShikimate dehydrogenase family protein
KeywordsOXIDOREDUCTASE / Rossmann-fold NAD(P)(+)-binding site / Shikimate dehydrogenase / NAD+ binding / Shikimate binding
Function / homology
Function and homology information


shikimate 3-dehydrogenase (NADP+) activity / nucleotide binding
Similarity search - Function
Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Shikimate dehydrogenase family protein
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGarcia, C. / Peek, J. / Petit, P. / Christendat, D.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Insights into the function of RifI2: structural and biochemical investigation of a new shikimate dehydrogenase family protein.
Authors: Peek, J. / Garcia, C. / Lee, J. / Christendat, D.
History
DepositionApr 8, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionApr 17, 2013ID: 3TUM
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Shikimate dehydrogenase family protein
B: Shikimate dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,87211
Polymers56,1922
Non-polymers1,6799
Water4,666259
1
A: Shikimate dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9245
Polymers28,0961
Non-polymers8284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Shikimate dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9476
Polymers28,0961
Non-polymers8515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Shikimate dehydrogenase family protein
hetero molecules

A: Shikimate dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,87211
Polymers56,1922
Non-polymers1,6799
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area5050 Å2
ΔGint-67 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.437, 76.688, 153.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Shikimate dehydrogenase family protein


Mass: 28096.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: pp2608, PP_2608 / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q88JP1
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.1M sodium citrate, 0.2M ammonium acetate, 20% PEG 8000 , pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.15→19.22 Å / Num. all: 29340 / Num. obs: 29145 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.083 / Net I/σ(I): 17.5
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4202 / Rsym value: 0.559 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: dev_237)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→19.22 Å / SU ML: 0.3 / σ(F): 0.02 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1399 5.07 %RANDOM
Rwork0.1791 ---
obs0.1821 27601 94.15 %-
all-29340 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.413 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.032 Å20 Å20 Å2
2---0.0863 Å2-0 Å2
3---0.0543 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 95 259 4236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074081
X-RAY DIFFRACTIONf_angle_d1.2725570
X-RAY DIFFRACTIONf_dihedral_angle_d26.3781546
X-RAY DIFFRACTIONf_chiral_restr0.065649
X-RAY DIFFRACTIONf_plane_restr0.013732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.22680.25721310.21122371X-RAY DIFFRACTION87
2.2268-2.31580.29141180.21232391X-RAY DIFFRACTION88
2.3158-2.4210.28191280.20932474X-RAY DIFFRACTION90
2.421-2.54840.25591230.20762526X-RAY DIFFRACTION92
2.5484-2.70760.28441580.19832571X-RAY DIFFRACTION94
2.7076-2.9160.28051320.20542642X-RAY DIFFRACTION95
2.916-3.20820.24651450.18672714X-RAY DIFFRACTION97
3.2082-3.66970.22551420.16122776X-RAY DIFFRACTION99
3.6697-4.61280.19141480.14392809X-RAY DIFFRACTION99
4.6128-19.2250.19811740.14862928X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -13.9082 Å / Origin y: 13.7382 Å / Origin z: -18.9135 Å
111213212223313233
T0.0254 Å2-0.0011 Å20.0158 Å2-0.0317 Å20.0195 Å2--0.0461 Å2
L0.1616 °20.175 °2-0.0462 °2-0.1489 °2-0.0406 °2--0.2722 °2
S-0.0184 Å °0.0274 Å °-0.0424 Å °-0.037 Å °0.0546 Å °-0.0486 Å °0.0283 Å °-0.064 Å °-0.0299 Å °
Refinement TLS groupSelection details: all

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