HEADER PROTEIN BINDING 28-NOV-01 1KH0 TITLE ACCURATE COMPUTER BASE DESIGN OF A NEW BACKBONE CONFORMATION IN THE TITLE 2 SECOND TURN OF PROTEIN L COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN L; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: B1 DOMAIN (RESIDUES 111-173); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FINEGOLDIA MAGNA; SOURCE 3 ORGANISM_TAXID: 334413; SOURCE 4 STRAIN: ATCC 29328; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS PROTEIN L B1 DOMAIN, COMPUTATIONAL BASED PROTEIN DESIGN, TYPE 1' BETA KEYWDS 2 TURN, EXTENSIVE AMINO ACID MUTATIONS., PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.W.O'NEILL,B.KUHLMAN,D.E.KIM,K.Y.ZHANG,D.BAKER REVDAT 8 16-AUG-23 1KH0 1 REMARK REVDAT 7 27-OCT-21 1KH0 1 SEQADV REVDAT 6 11-OCT-17 1KH0 1 REMARK REVDAT 5 13-JUL-11 1KH0 1 VERSN REVDAT 4 24-FEB-09 1KH0 1 VERSN REVDAT 3 01-APR-03 1KH0 1 JRNL REVDAT 2 07-AUG-02 1KH0 1 SEQADV REVDAT 1 23-JAN-02 1KH0 0 JRNL AUTH B.KUHLMAN,J.W.O'NEILL,D.E.KIM,K.Y.ZHANG,D.BAKER JRNL TITL ACCURATE COMPUTER-BASED DESIGN OF A NEW BACKBONE JRNL TITL 2 CONFORMATION IN THE SECOND TURN OF PROTEIN L. JRNL REF J.MOL.BIOL. V. 315 471 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11786026 JRNL DOI 10.1006/JMBI.2001.5229 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1027037.390 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 11579 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) : 0.197 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1134 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1683 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 171 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.22000 REMARK 3 B22 (A**2) : -3.83000 REMARK 3 B33 (A**2) : -2.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 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) : 1.740 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.720 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.800 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.190 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 54.20 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KH0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014949. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11610 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 36.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : 0.25200 REMARK 200 FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1HZ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M SODIUM CITRATE, 100MM CACODYLATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.31100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.69100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.77100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.69100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.31100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.77100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 42 CG CD CE NZ REMARK 470 ARG A 52 CG CD NE CZ NH1 NH2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HZ5 RELATED DB: PDB REMARK 900 MONOMERIC WT PROTEIN L, B1 DOMAIN WITH A Y47W MUTATION REMARK 900 RELATED ID: 1HZ6 RELATED DB: PDB REMARK 900 MONOMERIC WT PROTEIN L, B1 DOMAIN WITH A Y47W MUTATION, ZN- REMARK 900 COORDINATED HIS-TAG DBREF 1KH0 A 2 66 UNP Q51912 Q51912_PEPMA 111 173 DBREF 1KH0 B 2 66 UNP Q51912 Q51912_PEPMA 111 173 SEQADV 1KH0 LYS A 26 UNP Q51912 PHE 135 ENGINEERED MUTATION SEQADV 1KH0 LEU A 30 UNP Q51912 THR 139 ENGINEERED MUTATION SEQADV 1KH0 VAL A 33 UNP Q51912 ALA 142 ENGINEERED MUTATION SEQADV 1KH0 LEU A 34 UNP Q51912 TYR 143 ENGINEERED MUTATION SEQADV 1KH0 TRP A 47 UNP Q51912 TYR 156 ENGINEERED MUTATION SEQADV 1KH0 ILE A 49 UNP Q51912 VAL 158 ENGINEERED MUTATION SEQADV 1KH0 LYS A 51 UNP Q51912 INSERTION SEQADV 1KH0 ARG A 52 UNP Q51912 INSERTION SEQADV 1KH0 THR A 54 UNP Q51912 ALA 161 ENGINEERED MUTATION SEQADV 1KH0 ASN A 55 UNP Q51912 ASP 162 ENGINEERED MUTATION SEQADV 1KH0 GLY A 56 UNP Q51912 LYS 163 ENGINEERED MUTATION SEQADV 1KH0 VAL A 57 UNP Q51912 GLY 164 ENGINEERED MUTATION SEQADV 1KH0 ILE A 58 UNP Q51912 TYR 165 ENGINEERED MUTATION SEQADV 1KH0 ILE A 59 UNP Q51912 THR 166 ENGINEERED MUTATION SEQADV 1KH0 LYS B 26 UNP Q51912 PHE 135 ENGINEERED MUTATION SEQADV 1KH0 LEU B 30 UNP Q51912 THR 139 ENGINEERED MUTATION SEQADV 1KH0 VAL B 33 UNP Q51912 ALA 142 ENGINEERED MUTATION SEQADV 1KH0 LEU B 34 UNP Q51912 TYR 143 ENGINEERED MUTATION SEQADV 1KH0 TRP B 47 UNP Q51912 TYR 156 ENGINEERED MUTATION SEQADV 1KH0 ILE B 49 UNP Q51912 VAL 158 ENGINEERED MUTATION SEQADV 1KH0 LYS B 51 UNP Q51912 INSERTION SEQADV 1KH0 ARG B 52 UNP Q51912 INSERTION SEQADV 1KH0 THR B 54 UNP Q51912 ALA 161 ENGINEERED MUTATION SEQADV 1KH0 ASN B 55 UNP Q51912 ASP 162 ENGINEERED MUTATION SEQADV 1KH0 GLY B 56 UNP Q51912 LYS 163 ENGINEERED MUTATION SEQADV 1KH0 VAL B 57 UNP Q51912 GLY 164 ENGINEERED MUTATION SEQADV 1KH0 ILE B 58 UNP Q51912 TYR 165 ENGINEERED MUTATION SEQADV 1KH0 ILE B 59 UNP Q51912 THR 166 ENGINEERED MUTATION SEQRES 1 A 65 GLU GLU VAL THR ILE LYS ALA ASN LEU ILE PHE ALA ASN SEQRES 2 A 65 GLY SER THR GLN THR ALA GLU PHE LYS GLY THR LYS GLU SEQRES 3 A 65 LYS ALA LEU SER GLU VAL LEU ALA TYR ALA ASP THR LEU SEQRES 4 A 65 LYS LYS ASP ASN GLY GLU TRP THR ILE ASP LYS ARG VAL SEQRES 5 A 65 THR ASN GLY VAL ILE ILE LEU ASN ILE LYS PHE ALA GLY SEQRES 1 B 65 GLU GLU VAL THR ILE LYS ALA ASN LEU ILE PHE ALA ASN SEQRES 2 B 65 GLY SER THR GLN THR ALA GLU PHE LYS GLY THR LYS GLU SEQRES 3 B 65 LYS ALA LEU SER GLU VAL LEU ALA TYR ALA ASP THR LEU SEQRES 4 B 65 LYS LYS ASP ASN GLY GLU TRP THR ILE ASP LYS ARG VAL SEQRES 5 B 65 THR ASN GLY VAL ILE ILE LEU ASN ILE LYS PHE ALA GLY FORMUL 3 HOH *80(H2 O) HELIX 1 1 LYS A 26 GLY A 45 1 20 HELIX 2 2 THR B 25 GLY B 45 1 21 SHEET 1 A 4 THR A 17 THR A 25 0 SHEET 2 A 4 GLU A 3 ILE A 11 -1 N LEU A 10 O GLN A 18 SHEET 3 A 4 VAL A 57 PHE A 64 1 O ILE A 58 N LYS A 7 SHEET 4 A 4 TRP A 47 THR A 54 -1 N ARG A 52 O ILE A 59 SHEET 1 B 4 THR B 17 GLY B 24 0 SHEET 2 B 4 VAL B 4 ILE B 11 -1 N VAL B 4 O GLY B 24 SHEET 3 B 4 VAL B 57 PHE B 64 1 O LEU B 60 N ASN B 9 SHEET 4 B 4 TRP B 47 THR B 54 -1 N ARG B 52 O ILE B 59 CRYST1 38.622 55.542 67.382 90.00 90.00 90.00 P 21 21 21 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 0.025892 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014841 0.00000