HEADER DE NOVO PROTEIN 10-MAR-04 1SNE TITLE AN OLIGOMERIC DOMAIN-SWAPPED BETA-BETA-ALPHA MINI-PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TETRAMERIC BETA-BETA-ALPHA MINI-PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BBAT; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. KEYWDS PROTEIN DESIGN, DOMAIN SWAPPING, MINI-PROTEIN, OLIGOMERIZATION, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.H.ALI,E.PEISACH,K.N.ALLEN,B.IMPERIALI REVDAT 6 08-MAY-24 1SNE 1 ATOM REVDAT 5 15-NOV-23 1SNE 1 REMARK LINK ATOM REVDAT 4 24-FEB-09 1SNE 1 VERSN REVDAT 3 26-OCT-04 1SNE 1 MODRES REVDAT 2 24-AUG-04 1SNE 1 JRNL REVDAT 1 17-AUG-04 1SNE 0 JRNL AUTH M.H.ALI,E.PEISACH,K.N.ALLEN,B.IMPERIALI JRNL TITL X-RAY STRUCTURE ANALYSIS OF A DESIGNED OLIGOMERIC JRNL TITL 2 MINIPROTEIN REVEALS A DISCRETE QUATERNARY ARCHITECTURE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 12183 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15302930 JRNL DOI 10.1073/PNAS.0401245101 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1233606.430 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 74.3 REMARK 3 NUMBER OF REFLECTIONS : 7769 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 786 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 21.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 351 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 29 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.81000 REMARK 3 B22 (A**2) : 2.18000 REMARK 3 B33 (A**2) : -1.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 58.19 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1SNE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978031, 0.97902, 0.949320 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7811 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.4 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 16.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.08500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES-NA, 10% V/V I-PROPANOL, REMARK 280 20% W/V PEG 4000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 28.95600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 10.66250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.95600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 10.66250 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 16.58009 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -27.24803 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 87 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 89 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ILE A 103 N - CA - C ANGL. DEV. = -16.5 DEGREES 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 IPA A 123 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SN9 RELATED DB: PDB REMARK 900 RELATED ID: 1SNA RELATED DB: PDB DBREF 1SNE A 100 122 PDB 1SNE 1SNE 100 122 DBREF 1SNE B 200 222 PDB 1SNE 1SNE 200 222 SEQRES 1 A 23 ACE TYR ARG ILE DPR SER TYR ASP PHE DAL ASP GLU LEU SEQRES 2 A 23 ALA LYS LEU LEU ARG MSO ALA DBZ GLY NH2 SEQRES 1 B 23 ACE TYR ARG ILE DPR SER TYR ASP PHE DAL ASP GLU LEU SEQRES 2 B 23 ALA LYS LEU LEU ARG MSO ALA DBZ GLY NH2 MODRES 1SNE DPR A 104 PRO D-PROLINE MODRES 1SNE DAL A 109 ALA D-ALANINE MODRES 1SNE MSO A 118 MET SELENOMETHIONINE SELENOXIDE MODRES 1SNE DBZ A 120 ALA 3-(BENZOYLAMINO)-L-ALANINE MODRES 1SNE DPR B 204 PRO D-PROLINE MODRES 1SNE DAL B 209 ALA D-ALANINE MODRES 1SNE MSO B 218 MET SELENOMETHIONINE SELENOXIDE MODRES 1SNE DBZ B 220 ALA 3-(BENZOYLAMINO)-L-ALANINE HET ACE A 100 3 HET DPR A 104 7 HET DAL A 109 5 HET MSO A 118 18 HET DBZ A 120 14 HET NH2 A 122 1 HET ACE B 200 3 HET DPR B 204 7 HET DAL B 209 5 HET MSO B 218 18 HET DBZ B 220 14 HET NH2 B 222 1 HET IPA A 123 4 HETNAM ACE ACETYL GROUP HETNAM DPR D-PROLINE HETNAM DAL D-ALANINE HETNAM MSO SELENOMETHIONINE SELENOXIDE HETNAM DBZ 3-(BENZOYLAMINO)-L-ALANINE HETNAM NH2 AMINO GROUP HETNAM IPA ISOPROPYL ALCOHOL HETSYN IPA 2-PROPANOL FORMUL 1 ACE 2(C2 H4 O) FORMUL 1 DPR 2(C5 H9 N O2) FORMUL 1 DAL 2(C3 H7 N O2) FORMUL 1 MSO 2(C5 H11 N O3 SE) FORMUL 1 DBZ 2(C10 H12 N2 O3) FORMUL 1 NH2 2(H2 N) FORMUL 3 IPA C3 H8 O FORMUL 4 HOH *69(H2 O) HELIX 1 1 PHE A 108 GLY A 121 1 14 HELIX 2 2 PHE B 208 GLY B 221 1 14 SHEET 1 A 2 ARG A 102 ILE A 103 0 SHEET 2 A 2 TYR A 106 ASP A 107 -1 O TYR A 106 N ILE A 103 SHEET 1 B 2 ARG B 202 ILE B 203 0 SHEET 2 B 2 TYR B 206 ASP B 207 -1 O TYR B 206 N ILE B 203 LINK C ACE A 100 N TYR A 101 1555 1555 1.33 LINK C ILE A 103 N DPR A 104 1555 1555 1.34 LINK C DPR A 104 N SER A 105 1555 1555 1.33 LINK C PHE A 108 N DAL A 109 1555 1555 1.33 LINK C DAL A 109 N ASP A 110 1555 1555 1.33 LINK C ARG A 117 N AMSO A 118 1555 1555 1.33 LINK C ARG A 117 N BMSO A 118 1555 1555 1.33 LINK C AMSO A 118 N ALA A 119 1555 1555 1.33 LINK C BMSO A 118 N ALA A 119 1555 1555 1.33 LINK C ALA A 119 N DBZ A 120 1555 1555 1.33 LINK C DBZ A 120 N GLY A 121 1555 1555 1.33 LINK C GLY A 121 N NH2 A 122 1555 1555 1.33 LINK C ACE B 200 N TYR B 201 1555 1555 1.33 LINK C ILE B 203 N DPR B 204 1555 1555 1.34 LINK C DPR B 204 N SER B 205 1555 1555 1.33 LINK C PHE B 208 N DAL B 209 1555 1555 1.33 LINK C DAL B 209 N ASP B 210 1555 1555 1.33 LINK C ARG B 217 N AMSO B 218 1555 1555 1.33 LINK C ARG B 217 N BMSO B 218 1555 1555 1.33 LINK C AMSO B 218 N ALA B 219 1555 1555 1.33 LINK C BMSO B 218 N ALA B 219 1555 1555 1.33 LINK C ALA B 219 N DBZ B 220 1555 1555 1.33 LINK C DBZ B 220 N GLY B 221 1555 1555 1.31 LINK C GLY B 221 N NH2 B 222 1555 1555 1.34 SITE 1 AC1 5 HOH A 82 TYR A 101 LEU A 116 HOH B 21 SITE 2 AC1 5 DAL B 209 CRYST1 57.912 21.325 31.896 90.00 121.32 90.00 C 1 2 1 8 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 0.017268 0.000000 0.010507 0.00000 SCALE2 0.000000 0.046893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036700 0.00000 HETATM 1 C ACE A 100 13.993 9.763 -22.282 1.00 12.98 C HETATM 2 O ACE A 100 13.999 10.088 -23.469 1.00 14.74 O HETATM 3 CH3 ACE A 100 14.323 8.363 -21.838 1.00 14.47 C