HEADER DE NOVO PROTEIN 14-OCT-05 1VRZ TITLE HELIX TURN HELIX MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED 21 RESIDUE PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PEPTIDE IS CHEMICALY SYNTHEISED BY SOLID PHASE SOURCE 4 MANUAL PEPTIDE SYNTHESIS USING FMOC CHEMISTRY. KEYWDS HTH, HELIX-TURN-HELIX MOTIF, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR RUDRESH,S.RAMAKUMAR,U.A.RAMAGOPAL,Y.INAI,D.SAHAL REVDAT 3 27-DEC-23 1VRZ 1 REMARK LINK REVDAT 2 24-FEB-09 1VRZ 1 VERSN REVDAT 1 01-NOV-05 1VRZ 0 SPRSDE 01-NOV-05 1VRZ 1Q4F JRNL AUTH RUDRESH,S.RAMAKUMAR,U.A.RAMAGOPAL,Y.INAI,S.GOEL,D.SAHAL, JRNL AUTH 2 V.S.CHAUHAN JRNL TITL DE NOVO DESIGN AND CHARACTERIZATION OF A HELICAL HAIRPIN JRNL TITL 2 EICOSAPEPTIDE; EMERGENCE OF AN ANION RECEPTOR IN THE LINKER JRNL TITL 3 REGION. JRNL REF STRUCTURE V. 12 389 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 15016355 JRNL DOI 10.1016/J.STR.2004.02.014 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.125 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.125 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7382 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.125 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6913 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 158 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 172.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 122.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1532 REMARK 3 NUMBER OF RESTRAINTS : 1 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 1VRZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000003001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6913 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 12.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.23900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 20.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ACETIC ACID AND ETHANOL (1:1 V/V) REMARK 280 MIXTURE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 23.32550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 10.49350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.32550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 10.49350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 28 O HOH A 29 4647 1.64 REMARK 500 O HOH A 26 O HOH A 28 4657 1.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ACE A 1 C GLY A 2 N -0.144 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 24 DBREF 1VRZ A 1 23 PDB 1VRZ 1VRZ 1 23 SEQRES 1 A 23 ACE GLY 23F ALA 23F 23F ALA 23F 23F ALA GLY GLY GLY SEQRES 2 A 23 GLY 23F ALA LEU 23F ALA LEU 23F ALA NH2 MODRES 1VRZ 23F A 3 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID MODRES 1VRZ 23F A 5 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID MODRES 1VRZ 23F A 6 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID MODRES 1VRZ 23F A 8 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID MODRES 1VRZ 23F A 9 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID MODRES 1VRZ 23F A 15 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID MODRES 1VRZ 23F A 18 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID MODRES 1VRZ 23F A 21 PHE (2Z)-2-AMINO-3-PHENYLACRYLIC ACID HET ACE A 1 6 HET 23F A 3 18 HET 23F A 5 18 HET 23F A 6 18 HET 23F A 8 18 HET 23F A 9 18 HET 23F A 15 18 HET 23F A 18 18 HET 23F A 21 18 HET NH2 A 23 3 HET ACT A 24 4 HETNAM ACE ACETYL GROUP HETNAM 23F (2Z)-2-AMINO-3-PHENYLACRYLIC ACID HETNAM NH2 AMINO GROUP HETNAM ACT ACETATE ION HETSYN 23F DEHYDROPHENYLALANINE FORMUL 1 ACE C2 H4 O FORMUL 1 23F 8(C9 H9 N O2) FORMUL 1 NH2 H2 N FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *13(H2 O) HELIX 1 1 GLY A 2 GLY A 12 5 11 HELIX 2 2 GLY A 13 ALA A 22 5 10 LINK C ACE A 1 N GLY A 2 1555 1555 1.19 LINK C GLY A 2 N 23F A 3 1555 1555 1.34 LINK C 23F A 3 N ALA A 4 1555 1555 1.39 LINK C ALA A 4 N 23F A 5 1555 1555 1.37 LINK C 23F A 5 N 23F A 6 1555 1555 1.36 LINK C 23F A 6 N ALA A 7 1555 1555 1.35 LINK C ALA A 7 N 23F A 8 1555 1555 1.34 LINK C 23F A 8 N 23F A 9 1555 1555 1.38 LINK C 23F A 9 N ALA A 10 1555 1555 1.38 LINK C GLY A 14 N 23F A 15 1555 1555 1.37 LINK C 23F A 15 N ALA A 16 1555 1555 1.39 LINK C LEU A 17 N 23F A 18 1555 1555 1.38 LINK C 23F A 18 N ALA A 19 1555 1555 1.36 LINK C LEU A 20 N 23F A 21 1555 1555 1.33 LINK C 23F A 21 N ALA A 22 1555 1555 1.35 LINK C ALA A 22 N NH2 A 23 1555 1555 1.34 SITE 1 AC1 5 23F A 5 23F A 9 GLY A 12 GLY A 13 SITE 2 AC1 5 ALA A 16 CRYST1 46.651 20.987 14.449 90.00 94.66 90.00 C 1 2 1 4 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 0.021436 0.000000 0.001748 0.00000 SCALE2 0.000000 0.047649 0.000000 0.00000 SCALE3 0.000000 0.000000 0.069439 0.00000 HETATM 1 C ACE A 1 24.407 21.183 7.464 1.00 12.45 C HETATM 2 O ACE A 1 24.433 21.816 6.380 1.00 17.15 O HETATM 3 CH3 ACE A 1 24.407 21.768 8.921 1.00 15.34 C HETATM 4 H1 ACE A 1 24.398 22.727 8.881 1.00 23.00 H HETATM 5 H2 ACE A 1 25.195 21.474 9.384 1.00 23.00 H HETATM 6 H3 ACE A 1 23.627 21.460 9.389 1.00 23.00 H