HEADER PLANT PROTEIN 22-JUN-14 4TTN TITLE QUASI-RACEMIC STRUCTURE OF [G6A]KALATA B1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: KALATA-B1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: D-KALATA B1; COMPND 8 CHAIN: B; COMPND 9 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: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS CYCLIC PEPTIDE, DISULFIDE BONDS, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.K.WANG,G.J.KING,D.J.CRAIK REVDAT 3 27-DEC-23 4TTN 1 SOURCE JRNL REMARK LINK REVDAT 2 22-OCT-14 4TTN 1 JRNL REVDAT 1 10-SEP-14 4TTN 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. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 20417 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 25.3504 - 3.0128 0.97 1364 148 0.2206 0.2145 REMARK 3 2 3.0128 - 2.3919 0.96 1338 146 0.2206 0.2343 REMARK 3 3 2.3919 - 2.0897 0.96 1357 146 0.2092 0.2308 REMARK 3 4 2.0897 - 1.8987 0.96 1342 147 0.2009 0.2671 REMARK 3 5 1.8987 - 1.7627 0.95 1327 144 0.1985 0.2163 REMARK 3 6 1.7627 - 1.6588 0.95 1356 147 0.2001 0.2138 REMARK 3 7 1.6588 - 1.5757 0.95 1299 141 0.1975 0.2080 REMARK 3 8 1.5757 - 1.5071 0.93 1322 143 0.1877 0.1881 REMARK 3 9 1.5071 - 1.4491 0.94 1308 142 0.2020 0.2208 REMARK 3 10 1.4491 - 1.3991 0.93 1296 141 0.2212 0.2634 REMARK 3 11 1.3991 - 1.3554 0.92 1287 141 0.2121 0.2945 REMARK 3 12 1.3554 - 1.3166 0.92 1308 142 0.2256 0.2398 REMARK 3 13 1.3166 - 1.2820 0.91 1301 141 0.2322 0.2732 REMARK 3 14 1.2820 - 1.2507 0.87 1212 131 0.2557 0.2274 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) : 13.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.33 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 : 0.007 451 REMARK 3 ANGLE : 1.302 620 REMARK 3 CHIRALITY : 0.056 78 REMARK 3 PLANARITY : 0.009 79 REMARK 3 DIHEDRAL : 12.432 160 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 4TTN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202141. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 25.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.13800 REMARK 200 R SYM FOR SHELL (I) : 0.13800 REMARK 200 FOR SHELL : 5.500 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 (%): 29.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14% W/V (+/-)-2-METHYL-2,4 REMARK 280 -PENTANEDIOL, 4% V/V 1,3-PROPANEDIOL, VAPOR DIFFUSION, HANGING REMARK 280 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 O HOH A 129 O HOH B 226 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 115 O HOH B 203 28710 2.12 REMARK 500 O HOH A 101 O HOH B 208 1565 2.14 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 DCY B 9 -56.25 140.96 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 MPD B 101 DBREF 4TTN A 1 29 UNP P56254 KAB1_OLDAF 89 117 DBREF 4TTN B 1 29 PDB 4TTN 4TTN 1 29 SEQADV 4TTN ALA A 6 UNP P56254 GLY 94 ENGINEERED MUTATION SEQRES 1 A 29 GLY LEU PRO VAL CYS ALA 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 11 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 19 HET DSG B 29 8 HET MPD B 101 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 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL 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 MPD C6 H14 O2 FORMUL 4 HOH *62(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 2.05 SSBOND 2 CYS A 9 CYS A 21 1555 1555 2.05 SSBOND 3 CYS A 14 CYS A 26 1555 1555 2.05 SSBOND 4 DCY B 5 DCY B 19 1555 1555 2.05 SSBOND 5 DCY B 9 DCY B 21 1555 1555 2.04 SSBOND 6 DCY B 14 DCY B 26 1555 1555 2.04 LINK N GLY A 1 C ASN A 29 1555 1555 1.37 LINK C GLY B 1 N DLE B 2 1555 1555 1.33 LINK N GLY B 1 C DSG B 29 1555 1555 1.34 LINK C DLE B 2 N DPR B 3 1555 1555 1.34 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 1.34 LINK C DTH B 13 N DCY B 14 1555 1555 1.34 LINK C DCY B 14 N DSG B 15 1555 1555 1.33 LINK C DSG B 15 N DTH B 16 1555 1555 1.32 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 1.33 LINK C DTR B 23 N DPR B 24 1555 1555 1.35 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 1.32 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 5.36 CISPEP 2 DTR B 23 DPR B 24 0 -7.16 SITE 1 AC1 1 DVA B 4 CRYST1 22.186 25.923 37.713 93.80 106.59 99.91 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 0.045073 0.007871 0.014500 0.00000 SCALE2 0.000000 0.039159 0.004822 0.00000 SCALE3 0.000000 0.000000 0.027877 0.00000