HEADER PLANT PROTEIN 22-JUN-14 4TTM TITLE RACEMIC STRUCTURE OF KALATA B1 (KB1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: KALATA-B1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: D-KALATA B1; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: OLDENLANDIA AFFINIS; SOURCE 4 ORGANISM_TAXID: 60225; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: OLDENLANDIA AFFINIS; SOURCE 8 ORGANISM_TAXID: 60225 KEYWDS CYCLIC PEPTIDE, DISULFIDE BONDS, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.K.WANG,G.J.KING,D.J.CRAIK REVDAT 6 27-DEC-23 4TTM 1 LINK REVDAT 5 01-JAN-20 4TTM 1 LINK REVDAT 4 06-SEP-17 4TTM 1 REMARK REVDAT 3 20-JUL-16 4TTM 1 REMARK REVDAT 2 22-OCT-14 4TTM 1 SOURCE REVDAT 1 10-SEP-14 4TTM 0 JRNL AUTH C.K.WANG,G.J.KING,S.E.NORTHFIELD,P.G.OJEDA,D.J.CRAIK JRNL TITL RACEMIC AND QUASI-RACEMIC X-RAY STRUCTURES OF CYCLIC JRNL TITL 2 DISULFIDE-RICH PEPTIDE DRUG SCAFFOLDS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 53 11236 2014 JRNL REFN ESSN 1521-3773 JRNL PMID 25168664 JRNL DOI 10.1002/ANIE.201406563 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 5913 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 591 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 22.0529 - 3.0142 0.98 1380 154 0.2153 0.2375 REMARK 3 2 3.0142 - 2.3934 0.95 1338 148 0.2219 0.2921 REMARK 3 3 2.3934 - 2.0911 0.94 1330 148 0.2262 0.3083 REMARK 3 4 2.0911 - 1.9001 0.92 1274 141 0.2234 0.3311 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 435 REMARK 3 ANGLE : 1.199 596 REMARK 3 CHIRALITY : 0.073 74 REMARK 3 PLANARITY : 0.007 78 REMARK 3 DIHEDRAL : 7.336 152 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4TTM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202133. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : CU FINE FOCUS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 25.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.940 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.88 REMARK 200 R MERGE FOR SHELL (I) : 0.40900 REMARK 200 R SYM FOR SHELL (I) : 0.40900 REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% W/V (+/-)-2-METHYL-2,4 REMARK 280 -PENTANEDIOL, 4% V/V 1,3-PROPANEDIOL OR 14% W/V (+/-)-2-METHYL-2, REMARK 280 4-PENTANEDIOL, 5% W/V POLYETHYLENE GLYCOL 8,000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P -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 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NH2 DAR B 28 O HOH B 101 2.15 REMARK 500 REMARK 500 REMARK: NULL DBREF 4TTM A 1 29 UNP P56254 KAB1_OLDAF 89 117 DBREF 4TTM B 1 29 PDB 4TTM 4TTM 1 29 SEQRES 1 A 29 GLY LEU PRO VAL CYS GLY GLU THR CYS VAL GLY GLY THR SEQRES 2 A 29 CYS ASN THR PRO GLY CYS THR CYS SER TRP PRO VAL CYS SEQRES 3 A 29 THR ARG ASN SEQRES 1 B 29 GLY DLE DPR DVA DCY GLY DGL DTH DCY DVA GLY GLY DTH SEQRES 2 B 29 DCY DSG DTH DPR GLY DCY DTH DCY DSN DTR DPR DVA DCY SEQRES 3 B 29 DTH DAR DSG HET DLE B 2 8 HET DPR B 3 7 HET DVA B 4 7 HET DCY B 5 6 HET DGL B 7 9 HET DTH B 8 7 HET DCY B 9 6 HET DVA B 10 7 HET DTH B 13 7 HET DCY B 14 6 HET DSG B 15 8 HET DTH B 16 7 HET DPR B 17 7 HET DCY B 19 6 HET DTH B 20 11 HET DCY B 21 6 HET DSN B 22 6 HET DTR B 23 14 HET DPR B 24 7 HET DVA B 25 7 HET DCY B 26 6 HET DTH B 27 7 HET DAR B 28 11 HET DSG B 29 8 HETNAM DLE D-LEUCINE HETNAM DPR D-PROLINE HETNAM DVA D-VALINE HETNAM DCY D-CYSTEINE HETNAM DGL D-GLUTAMIC ACID HETNAM DTH D-THREONINE HETNAM DSG D-ASPARAGINE HETNAM DSN D-SERINE HETNAM DTR D-TRYPTOPHAN HETNAM DAR D-ARGININE FORMUL 2 DLE C6 H13 N O2 FORMUL 2 DPR 3(C5 H9 N O2) FORMUL 2 DVA 3(C5 H11 N O2) FORMUL 2 DCY 6(C3 H7 N O2 S) FORMUL 2 DGL C5 H9 N O4 FORMUL 2 DTH 5(C4 H9 N O3) FORMUL 2 DSG 2(C4 H8 N2 O3) FORMUL 2 DSN C3 H7 N O3 FORMUL 2 DTR C11 H12 N2 O2 FORMUL 2 DAR C6 H15 N4 O2 1+ FORMUL 3 HOH *57(H2 O) SHEET 1 AA1 2 THR A 20 SER A 22 0 SHEET 2 AA1 2 VAL A 25 THR A 27 -1 O THR A 27 N THR A 20 SHEET 1 AA2 2 DTH B 20 DSN B 22 0 SHEET 2 AA2 2 DVA B 25 DTH B 27 -1 O DTH B 27 N DTH B 20 SSBOND 1 CYS A 5 CYS A 19 1555 1555 2.03 SSBOND 2 CYS A 9 CYS A 21 1555 1555 2.05 SSBOND 3 CYS A 14 CYS A 26 1555 1555 2.03 SSBOND 4 DCY B 5 DCY B 19 1555 1555 2.04 SSBOND 5 DCY B 9 DCY B 21 1555 1555 2.04 SSBOND 6 DCY B 14 DCY B 26 1555 1555 2.03 LINK N GLY A 1 C ASN A 29 1555 1555 1.38 LINK C GLY B 1 N DLE B 2 1555 1555 1.33 LINK N GLY B 1 C DSG B 29 1555 1555 1.35 LINK C DLE B 2 N DPR B 3 1555 1555 1.35 LINK C DPR B 3 N DVA B 4 1555 1555 1.33 LINK C DVA B 4 N DCY B 5 1555 1555 1.33 LINK C DCY B 5 N GLY B 6 1555 1555 1.33 LINK C GLY B 6 N DGL B 7 1555 1555 1.33 LINK C DGL B 7 N DTH B 8 1555 1555 1.33 LINK C DTH B 8 N DCY B 9 1555 1555 1.33 LINK C DCY B 9 N DVA B 10 1555 1555 1.33 LINK C DVA B 10 N GLY B 11 1555 1555 1.33 LINK C GLY B 12 N DTH B 13 1555 1555 1.33 LINK C DTH B 13 N DCY B 14 1555 1555 1.33 LINK C DCY B 14 N DSG B 15 1555 1555 1.33 LINK C DSG B 15 N DTH B 16 1555 1555 1.33 LINK C DTH B 16 N DPR B 17 1555 1555 1.34 LINK C DPR B 17 N GLY B 18 1555 1555 1.33 LINK C GLY B 18 N DCY B 19 1555 1555 1.33 LINK C DCY B 19 N DTH B 20 1555 1555 1.33 LINK C DTH B 20 N DCY B 21 1555 1555 1.33 LINK C DCY B 21 N DSN B 22 1555 1555 1.33 LINK C DSN B 22 N DTR B 23 1555 1555 1.34 LINK C DTR B 23 N DPR B 24 1555 1555 1.34 LINK C DPR B 24 N DVA B 25 1555 1555 1.33 LINK C DVA B 25 N DCY B 26 1555 1555 1.33 LINK C DCY B 26 N DTH B 27 1555 1555 1.33 LINK C DTH B 27 N DAR B 28 1555 1555 1.33 LINK C DAR B 28 N DSG B 29 1555 1555 1.33 CISPEP 1 TRP A 23 PRO A 24 0 4.27 CISPEP 2 DTR B 23 DPR B 24 0 -5.28 CRYST1 22.279 25.960 37.887 93.75 106.73 99.92 P -1 2 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 0.044884 0.007852 0.014560 0.00000 SCALE2 0.000000 0.039105 0.004806 0.00000 SCALE3 0.000000 0.000000 0.027768 0.00000