HEADER DE NOVO PROTEIN 18-MAR-07 2P6J TITLE FULL-SEQUENCE COMPUTATIONAL DESIGN AND SOLUTION STRUCTURE OF A TITLE 2 THERMOSTABLE PROTEIN VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED ENGRAILED HOMEODOMAIN VARIANT UVF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 3 ORGANISM_TAXID: 32644; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN, HELIX-TURN-HELIX, COMPUTATIONAL PROTEIN DESIGN, KEYWDS 2 ENGRAILED HOMEODOMAIN EXPDTA SOLUTION NMR NUMMDL 43 AUTHOR P.S.SHAH,G.K.HOM,S.A.ROSS,J.K.LASSILA,K.A.CROWHURST,S.L.MAYO REVDAT 4 16-MAR-22 2P6J 1 REMARK REVDAT 3 24-FEB-09 2P6J 1 VERSN REVDAT 2 28-AUG-07 2P6J 1 JRNL REVDAT 1 14-AUG-07 2P6J 0 JRNL AUTH P.S.SHAH,G.K.HOM,S.A.ROSS,J.K.LASSILA,K.A.CROWHURST,S.L.MAYO JRNL TITL FULL-SEQUENCE COMPUTATIONAL DESIGN AND SOLUTION STRUCTURE OF JRNL TITL 2 A THERMOSTABLE PROTEIN VARIANT. JRNL REF J.MOL.BIOL. V. 372 1 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17628593 JRNL DOI 10.1016/J.JMB.2007.06.032 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, ARIA 1.2 REMARK 3 AUTHORS : VARIAN (VNMR), NILGES, M. ET AL. (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1321 RESTRAINTS: 1245 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 57 ARE DIHEDRAL ANGLE RESTRAINTS AND 19 REMARK 3 DISTANCE RESTRAINTS ARE REMARK 3 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 2P6J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000042028. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 50 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : UNIFORM (RANDOM) LABELING WITH REMARK 210 13C, 15N: U-13C, U-15N, 95% H2O, REMARK 210 5% D2O; UNIFORM (RANDOM) REMARK 210 LABELING WITH 15N: U-15N, 95% REMARK 210 H2O, 5% D2O; UNIFORM (RANDOM) REMARK 210 LABELING WITH 13C, 15N: U-13C, U- REMARK 210 15N, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : ALIPHATIC 3D_13C REMARK 210 -SEPARATED_NOESY; AROMATIC 3D_ REMARK 210 13C-SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 4.0, ARIA 1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, DISTANCE REMARK 210 GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 43 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. HYDROGEN BOND RESTRAINTS WERE DERIVED FROM REMARK 210 PROTECTION FACTORS MEASURED BY H/D EXCHANGE. TORSION ANGLE REMARK 210 RESTRAINTS WERE DERIVED FROM J-COUPLING DATA (HNHA EXPERIMENT) REMARK 210 AND FROM TALOS PREDICTIONS. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HD2 PHE A 48 HE22 GLN A 50 1.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 TRP A 4 -169.77 -172.99 REMARK 500 1 HIS A 19 -161.52 -104.71 REMARK 500 1 ARG A 21 145.82 70.33 REMARK 500 1 PHE A 48 -76.27 -69.74 REMARK 500 1 GLU A 49 12.26 -155.33 REMARK 500 2 SER A 5 107.69 -57.17 REMARK 500 2 HIS A 19 -135.99 -140.06 REMARK 500 2 GLU A 47 40.41 -95.84 REMARK 500 2 GLU A 49 5.86 -69.95 REMARK 500 3 GLN A 3 -51.41 -168.66 REMARK 500 3 VAL A 16 -64.91 -97.13 REMARK 500 3 ARG A 21 178.76 67.09 REMARK 500 3 GLU A 47 34.86 -96.87 REMARK 500 4 GLN A 3 -63.04 -131.33 REMARK 500 4 VAL A 16 -70.24 -90.14 REMARK 500 4 GLN A 20 22.99 46.77 REMARK 500 4 ARG A 21 165.40 75.71 REMARK 500 4 PHE A 48 -71.10 -74.37 REMARK 500 5 GLN A 3 -51.66 -174.21 REMARK 500 5 HIS A 19 -169.78 -120.11 REMARK 500 5 ARG A 21 176.70 68.36 REMARK 500 5 ILE A 22 147.29 -172.14 REMARK 500 5 PHE A 45 -64.71 -94.03 REMARK 500 5 PHE A 48 -72.33 -58.36 REMARK 500 6 LYS A 2 173.63 69.56 REMARK 500 6 GLN A 3 -61.49 -121.22 REMARK 500 6 HIS A 19 52.60 -118.55 REMARK 500 6 GLN A 20 -71.72 67.98 REMARK 500 6 ARG A 21 176.15 167.36 REMARK 500 6 GLU A 47 44.01 -99.14 REMARK 500 7 GLN A 3 -62.83 -131.04 REMARK 500 7 HIS A 19 35.98 -92.27 REMARK 500 7 ARG A 21 123.88 66.76 REMARK 500 7 GLU A 49 -33.48 170.71 REMARK 500 8 GLN A 3 -51.10 179.57 REMARK 500 8 HIS A 19 -157.70 -86.59 REMARK 500 8 ARG A 21 135.49 69.83 REMARK 500 8 PHE A 48 -158.40 -76.15 REMARK 500 9 VAL A 16 -62.66 -92.74 REMARK 500 9 HIS A 19 -151.70 -130.98 REMARK 500 9 ARG A 21 -40.76 74.99 REMARK 500 9 ILE A 22 140.39 58.40 REMARK 500 9 PHE A 48 -72.42 -75.90 REMARK 500 9 GLU A 49 -31.17 -167.61 REMARK 500 10 GLN A 3 -67.53 -123.70 REMARK 500 10 ARG A 21 179.54 63.30 REMARK 500 10 PHE A 48 -73.09 -77.66 REMARK 500 10 GLU A 49 -39.63 -161.65 REMARK 500 11 HIS A 19 -166.27 -104.03 REMARK 500 11 GLN A 20 22.50 -79.97 REMARK 500 REMARK 500 THIS ENTRY HAS 202 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 FULL SEQUENCE WAS COMPUTATIONALLY DESIGNED. THE SEQUENCE IS REMARK 999 NOT AVAILABE IN UNIPROT DATABASE AT THE TIME OF PROCESSING. DBREF 2P6J A 1 52 PDB 2P6J 2P6J 1 52 SEQRES 1 A 52 MET LYS GLN TRP SER GLU ASN VAL GLU GLU LYS LEU LYS SEQRES 2 A 52 GLU PHE VAL LYS ARG HIS GLN ARG ILE THR GLN GLU GLU SEQRES 3 A 52 LEU HIS GLN TYR ALA GLN ARG LEU GLY LEU ASN GLU GLU SEQRES 4 A 52 ALA ILE ARG GLN PHE PHE GLU GLU PHE GLU GLN ARG LYS HELIX 1 1 SER A 5 LYS A 17 1 13 HELIX 2 2 THR A 23 GLY A 35 1 13 HELIX 3 3 ASN A 37 GLU A 47 1 11 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1