HEADER TOXIN 23-SEP-21 7SAP TITLE THE CTI-HOMOLOG PACIFASTIN CAVEAT 7SAP RESIDUES CYS A 31 AND LEU A 32 THAT ARE NEXT TO EACH OTHER CAVEAT 2 7SAP IN THE SAMPLE SEQUENCE ARE NOT PROPERLY LINKED: DISTANCE CAVEAT 3 7SAP BETWEEN C AND N IS 1.69 A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE PROTEASE INHIBITOR I/II-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRIBOLIUM CASTANEUM; SOURCE 3 ORGANISM_TAXID: 7070; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CTI-HOMOLOG, PACIFASTIN, CDP, CYSTINE-DENSE PEPTIDES, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR M.M.GEWE,R.K.STRONG REVDAT 2 18-OCT-23 7SAP 1 REMARK REVDAT 1 03-AUG-22 7SAP 0 JRNL AUTH Z.R.CROOK,E.J.GIRARD,G.P.SEVILLA,M.Y.BRUSNIAK,P.B.RUPERT, JRNL AUTH 2 D.J.FRIEND,M.M.GEWE,M.CLARKE,I.LIN,R.RUFF,F.PAKIAM,T.D.PHI, JRNL AUTH 3 A.BANDARANAYAKE,C.E.CORRENTI,A.J.MHYRE,N.W.NAIRN,R.K.STRONG, JRNL AUTH 4 J.M.OLSON JRNL TITL EX SILICO ENGINEERING OF CYSTINE-DENSE PEPTIDES YIELDING A JRNL TITL 2 POTENT BISPECIFIC T CELL ENGAGER. JRNL REF SCI TRANSL MED V. 14 N0402 2022 JRNL REFN ESSN 1946-6242 JRNL PMID 35584229 JRNL DOI 10.1126/SCITRANSLMED.ABN0402 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 68.9 REMARK 3 NUMBER OF REFLECTIONS : 2998 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 + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 167 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 25 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 7.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.1410 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 486 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.229 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.801 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 508 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 458 ; 0.001 ; 0.011 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 687 ; 1.631 ; 1.691 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1048 ; 1.414 ; 1.608 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 66 ; 8.117 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;27.231 ;18.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 77 ;12.163 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;16.348 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 74 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 591 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 129 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7SAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259936. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-16 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3164 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 25.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 69.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.6600 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7SAO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS GREW AFTER ~6 MONTHS FROM REMARK 280 SPARSE MATRIX SCREEN JCSG+ SUITE C10 (0.1 M MES PH 6.5, 25 % (W/ REMARK 280 V) PEG 8000), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.25100 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 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 232 O HOH B 227 2555 2.11 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 ASP A 11 -123.65 61.75 REMARK 500 ASP B 11 -115.76 59.49 REMARK 500 REMARK 500 REMARK: NULL DBREF 7SAP A -1 32 PDB 7SAP 7SAP -1 32 DBREF 7SAP B -1 32 PDB 7SAP 7SAP -1 32 SEQRES 1 A 34 GLY SER SER CYS GLN PRO GLY THR THR PHE ARG ARG ASP SEQRES 2 A 34 CYS ASN THR CYS VAL CYS ASN ARG ASP GLY THR ASN ALA SEQRES 3 A 34 ALA CYS THR LEU ARG ALA CYS LEU SEQRES 1 B 34 GLY SER SER CYS GLN PRO GLY THR THR PHE ARG ARG ASP SEQRES 2 B 34 CYS ASN THR CYS VAL CYS ASN ARG ASP GLY THR ASN ALA SEQRES 3 B 34 ALA CYS THR LEU ARG ALA CYS LEU HET GOL A 101 6 HET GOL B 101 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *62(H2 O) SHEET 1 AA1 3 THR A 7 ARG A 10 0 SHEET 2 AA1 3 ASN A 13 CYS A 17 -1 O CYS A 15 N PHE A 8 SHEET 3 AA1 3 ALA A 24 CYS A 26 -1 O ALA A 25 N VAL A 16 SHEET 1 AA2 3 THR B 7 ARG B 10 0 SHEET 2 AA2 3 ASN B 13 CYS B 17 -1 O ASN B 13 N ARG B 10 SHEET 3 AA2 3 ALA B 24 CYS B 26 -1 O ALA B 25 N VAL B 16 SSBOND 1 CYS A 2 CYS A 17 1555 1555 2.04 SSBOND 2 CYS A 12 CYS A 31 1555 1555 2.02 SSBOND 3 CYS A 15 CYS A 26 1555 1555 2.02 SSBOND 4 CYS B 2 CYS B 17 1555 1555 2.05 SSBOND 5 CYS B 12 CYS B 31 1555 1555 2.01 SSBOND 6 CYS B 15 CYS B 26 1555 1555 2.01 CRYST1 19.774 50.502 25.327 90.00 104.55 90.00 P 1 21 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 0.050571 0.000000 0.013127 0.00000 SCALE2 0.000000 0.019801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.040792 0.00000