HEADER PLANT PROTEIN 30-JAN-19 6NTT TITLE X-RAY CRYSTAL STRUCTURE OF SOYBEAN TRYPSIN INHIBITOR (KUNITZ) TITLE 2 COMPLEXED WITH 1,5-DISULFONYL NAPHTHALENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPSIN INHIBITOR A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: KUNITZ-TYPE TRYPSIN INHIBITOR A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 GENE: KTI3; SOURCE 6 EXPRESSION_SYSTEM: GLYCINE MAX; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 3847 KEYWDS SILVER BULLETS, LIGANDS, SYMMETRY, OLIGOMER, CRYSTALLIZATION, BUFFER, KEYWDS 2 PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.MCPHERSON REVDAT 3 11-OCT-23 6NTT 1 REMARK REVDAT 2 11-DEC-19 6NTT 1 JRNL REVDAT 1 20-MAR-19 6NTT 0 JRNL AUTH A.MCPHERSON,J.DAY,S.B.LARSON JRNL TITL LATTICE INTERACTIONS IN CRYSTALS OF SOYBEAN TRYPSIN JRNL TITL 2 INHIBITOR (KUNITZ) PRODUCED BY INCLUSION OF JRNL TITL 3 1,5-DISULFONYLNAPHTHALENE JRNL REF CRYST.GROWTH DES. V. 19 2963 2019 JRNL REFN ESSN 1528-7505 JRNL DOI 10.1021/ACS.CGD.9B00164 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 12813 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 656 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 943 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.4110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.29000 REMARK 3 B22 (A**2) : -1.71000 REMARK 3 B33 (A**2) : 3.46000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.697 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.378 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.391 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.498 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2971 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2680 ; 0.000 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4053 ; 1.284 ; 1.624 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6237 ; 1.100 ; 1.599 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 350 ; 8.191 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;33.460 ;23.161 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 474 ;15.304 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.478 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 363 ; 0.049 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3658 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 608 ; 0.000 ; 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): 1403 ; 2.074 ; 3.923 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1402 ; 2.074 ; 3.922 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1746 ; 3.302 ; 5.876 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1747 ; 3.302 ; 5.877 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1568 ; 2.284 ; 4.442 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1566 ; 2.283 ; 4.426 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2306 ; 3.731 ; 6.587 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 10703 ; 6.946 ;74.680 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 10704 ; 6.946 ;74.693 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 177 B 1 177 4513 0.18 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 177 REMARK 3 ORIGIN FOR THE GROUP (A): 12.7390 13.3710 44.0710 REMARK 3 T TENSOR REMARK 3 T11: 0.3244 T22: 0.0164 REMARK 3 T33: 0.2793 T12: -0.0369 REMARK 3 T13: -0.0172 T23: -0.0268 REMARK 3 L TENSOR REMARK 3 L11: 2.0520 L22: 4.5535 REMARK 3 L33: 4.8728 L12: -0.9566 REMARK 3 L13: 0.3895 L23: 1.1668 REMARK 3 S TENSOR REMARK 3 S11: 0.0393 S12: -0.0819 S13: -0.1890 REMARK 3 S21: 0.1194 S22: -0.0080 S23: 0.0711 REMARK 3 S31: 0.4036 S32: 0.0557 S33: -0.0312 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -8 B 177 REMARK 3 ORIGIN FOR THE GROUP (A): 29.7110 43.0320 57.7950 REMARK 3 T TENSOR REMARK 3 T11: 0.3634 T22: 0.0189 REMARK 3 T33: 0.3219 T12: -0.0145 REMARK 3 T13: -0.0816 T23: -0.0449 REMARK 3 L TENSOR REMARK 3 L11: 5.4807 L22: 4.6645 REMARK 3 L33: 5.2568 L12: -0.2567 REMARK 3 L13: -0.8071 L23: 2.5674 REMARK 3 S TENSOR REMARK 3 S11: -0.0275 S12: -0.1791 S13: 0.8272 REMARK 3 S21: -0.1165 S22: 0.0624 S23: -0.1266 REMARK 3 S31: -0.5494 S32: -0.1011 S33: -0.0348 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6NTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239377. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 6.3 - 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13649 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 32.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : 0.12400 REMARK 200 FOR THE DATA SET : 4.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 1AVU REMARK 200 REMARK 200 REMARK: THIN PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LYOPHILIZED PROTEIN DISSOLVED IN WATER REMARK 280 TO 25 MG/ML. SITTING DROP VAPOR DIFFUSION AGAINST RESERVOIRS OF REMARK 280 25% PEG 3350 WITH 0.10 M MES BUFFER PH 6.5. 3 UL DROPS COMPOSED REMARK 280 OF EQUAL AMOUNTS OF PROTEIN STOCK SOLUTION AND RESERVOIR REMARK 280 SUPPLEMENTED WITH 0.10 M 1,5-DISULFONYL NAPHTHALENE. REMARK 280 CRYSTALLIZATION TIME ABOUT 2 WEEKS., VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K 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 32.34000 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 MET A -23 REMARK 465 LYS A -22 REMARK 465 SER A -21 REMARK 465 THR A -20 REMARK 465 ILE A -19 REMARK 465 PHE A -18 REMARK 465 PHE A -17 REMARK 465 LEU A -16 REMARK 465 PHE A -15 REMARK 465 LEU A -14 REMARK 465 PHE A -13 REMARK 465 CYS A -12 REMARK 465 ALA A -11 REMARK 465 PHE A -10 REMARK 465 THR A -9 REMARK 465 THR A -8 REMARK 465 SER A -7 REMARK 465 TYR A -6 REMARK 465 LEU A -5 REMARK 465 PRO A -4 REMARK 465 SER A -3 REMARK 465 ALA A -2 REMARK 465 ILE A -1 REMARK 465 ALA A 0 REMARK 465 ASP A 125 REMARK 465 ASP A 126 REMARK 465 LYS A 178 REMARK 465 GLU A 179 REMARK 465 SER A 180 REMARK 465 LEU A 181 REMARK 465 ALA A 182 REMARK 465 LYS A 183 REMARK 465 LYS A 184 REMARK 465 ASN A 185 REMARK 465 HIS A 186 REMARK 465 GLY A 187 REMARK 465 LEU A 188 REMARK 465 SER A 189 REMARK 465 ARG A 190 REMARK 465 SER A 191 REMARK 465 GLU A 192 REMARK 465 MET B -23 REMARK 465 LYS B -22 REMARK 465 SER B -21 REMARK 465 THR B -20 REMARK 465 ILE B -19 REMARK 465 PHE B -18 REMARK 465 PHE B -17 REMARK 465 LEU B -16 REMARK 465 PHE B -15 REMARK 465 LEU B -14 REMARK 465 PHE B -13 REMARK 465 CYS B -12 REMARK 465 ALA B -11 REMARK 465 PHE B -10 REMARK 465 THR B -9 REMARK 465 THR B -8 REMARK 465 SER B -7 REMARK 465 TYR B -6 REMARK 465 LEU B -5 REMARK 465 PRO B -4 REMARK 465 SER B -3 REMARK 465 ALA B -2 REMARK 465 ILE B -1 REMARK 465 ALA B 0 REMARK 465 ASP B 142 REMARK 465 LYS B 178 REMARK 465 GLU B 179 REMARK 465 SER B 180 REMARK 465 LEU B 181 REMARK 465 ALA B 182 REMARK 465 LYS B 183 REMARK 465 LYS B 184 REMARK 465 ASN B 185 REMARK 465 HIS B 186 REMARK 465 GLY B 187 REMARK 465 LEU B 188 REMARK 465 SER B 189 REMARK 465 ARG B 190 REMARK 465 SER B 191 REMARK 465 GLU B 192 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 OD1 ASN B 130 NE2 GLN B 172 1.46 REMARK 500 O GLY A 108 OD1 ASN A 110 1.97 REMARK 500 CZ ARG B 30 OAD 21D B 201 2.09 REMARK 500 OG SER A 94 ND2 ASN A 110 2.09 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 ASN A 13 95.55 -59.56 REMARK 500 ARG A 63 23.82 86.93 REMARK 500 ILE A 107 -169.75 -111.62 REMARK 500 ASP A 142 -156.49 59.14 REMARK 500 ASP A 143 -122.30 57.09 REMARK 500 LYS A 144 74.97 54.14 REMARK 500 LYS A 167 123.86 -32.32 REMARK 500 ASN B 13 96.33 -63.20 REMARK 500 ALA B 25 25.70 -78.21 REMARK 500 ASP B 126 148.32 55.67 REMARK 500 ASN B 129 67.69 63.66 REMARK 500 ASN B 130 -165.07 -114.43 REMARK 500 GLN B 138 33.48 -97.00 REMARK 500 LYS B 167 124.63 -29.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 88 ILE A 89 -149.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 415 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A 416 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 417 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A 418 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 419 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 420 DISTANCE = 8.86 ANGSTROMS REMARK 525 HOH A 421 DISTANCE = 9.01 ANGSTROMS REMARK 525 HOH A 422 DISTANCE = 9.79 ANGSTROMS REMARK 525 HOH A 423 DISTANCE = 14.76 ANGSTROMS REMARK 525 HOH B 396 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH B 397 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH B 398 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH B 399 DISTANCE = 7.51 ANGSTROMS REMARK 525 HOH B 400 DISTANCE = 7.58 ANGSTROMS REMARK 525 HOH B 401 DISTANCE = 8.01 ANGSTROMS REMARK 525 HOH B 402 DISTANCE = 10.93 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 21D A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 21D B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 21D B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand GLN B 172 bound to ASN B REMARK 800 130 DBREF 6NTT A -23 192 UNP P01070 ITRA_SOYBN 1 216 DBREF 6NTT B -23 192 UNP P01070 ITRA_SOYBN 1 216 SEQRES 1 A 216 MET LYS SER THR ILE PHE PHE LEU PHE LEU PHE CYS ALA SEQRES 2 A 216 PHE THR THR SER TYR LEU PRO SER ALA ILE ALA ASP PHE SEQRES 3 A 216 VAL LEU ASP ASN GLU GLY ASN PRO LEU GLU ASN GLY GLY SEQRES 4 A 216 THR TYR TYR ILE LEU SER ASP ILE THR ALA PHE GLY GLY SEQRES 5 A 216 ILE ARG ALA ALA PRO THR GLY ASN GLU ARG CYS PRO LEU SEQRES 6 A 216 THR VAL VAL GLN SER ARG ASN GLU LEU ASP LYS GLY ILE SEQRES 7 A 216 GLY THR ILE ILE SER SER PRO TYR ARG ILE ARG PHE ILE SEQRES 8 A 216 ALA GLU GLY HIS PRO LEU SER LEU LYS PHE ASP SER PHE SEQRES 9 A 216 ALA VAL ILE MET LEU CYS VAL GLY ILE PRO THR GLU TRP SEQRES 10 A 216 SER VAL VAL GLU ASP LEU PRO GLU GLY PRO ALA VAL LYS SEQRES 11 A 216 ILE GLY GLU ASN LYS ASP ALA MET ASP GLY TRP PHE ARG SEQRES 12 A 216 LEU GLU ARG VAL SER ASP ASP GLU PHE ASN ASN TYR LYS SEQRES 13 A 216 LEU VAL PHE CYS PRO GLN GLN ALA GLU ASP ASP LYS CYS SEQRES 14 A 216 GLY ASP ILE GLY ILE SER ILE ASP HIS ASP ASP GLY THR SEQRES 15 A 216 ARG ARG LEU VAL VAL SER LYS ASN LYS PRO LEU VAL VAL SEQRES 16 A 216 GLN PHE GLN LYS LEU ASP LYS GLU SER LEU ALA LYS LYS SEQRES 17 A 216 ASN HIS GLY LEU SER ARG SER GLU SEQRES 1 B 216 MET LYS SER THR ILE PHE PHE LEU PHE LEU PHE CYS ALA SEQRES 2 B 216 PHE THR THR SER TYR LEU PRO SER ALA ILE ALA ASP PHE SEQRES 3 B 216 VAL LEU ASP ASN GLU GLY ASN PRO LEU GLU ASN GLY GLY SEQRES 4 B 216 THR TYR TYR ILE LEU SER ASP ILE THR ALA PHE GLY GLY SEQRES 5 B 216 ILE ARG ALA ALA PRO THR GLY ASN GLU ARG CYS PRO LEU SEQRES 6 B 216 THR VAL VAL GLN SER ARG ASN GLU LEU ASP LYS GLY ILE SEQRES 7 B 216 GLY THR ILE ILE SER SER PRO TYR ARG ILE ARG PHE ILE SEQRES 8 B 216 ALA GLU GLY HIS PRO LEU SER LEU LYS PHE ASP SER PHE SEQRES 9 B 216 ALA VAL ILE MET LEU CYS VAL GLY ILE PRO THR GLU TRP SEQRES 10 B 216 SER VAL VAL GLU ASP LEU PRO GLU GLY PRO ALA VAL LYS SEQRES 11 B 216 ILE GLY GLU ASN LYS ASP ALA MET ASP GLY TRP PHE ARG SEQRES 12 B 216 LEU GLU ARG VAL SER ASP ASP GLU PHE ASN ASN TYR LYS SEQRES 13 B 216 LEU VAL PHE CYS PRO GLN GLN ALA GLU ASP ASP LYS CYS SEQRES 14 B 216 GLY ASP ILE GLY ILE SER ILE ASP HIS ASP ASP GLY THR SEQRES 15 B 216 ARG ARG LEU VAL VAL SER LYS ASN LYS PRO LEU VAL VAL SEQRES 16 B 216 GLN PHE GLN LYS LEU ASP LYS GLU SER LEU ALA LYS LYS SEQRES 17 B 216 ASN HIS GLY LEU SER ARG SER GLU HET 21D A 201 36 HET MES A 202 24 HET 21D B 201 36 HET 21D B 202 36 HET MES B 203 12 HET MES B 204 12 HETNAM 21D NAPHTHALENE-1,5-DISULFONIC ACID HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 3 21D 3(C10 H8 O6 S2) FORMUL 4 MES 3(C6 H13 N O4 S) FORMUL 9 HOH *225(H2 O) HELIX 1 AA1 ILE A 83 VAL A 87 5 5 HELIX 2 AA2 ILE B 83 VAL B 87 5 5 SHEET 1 AA1 9 ILE A 29 ALA A 32 0 SHEET 2 AA1 9 THR A 42 GLN A 45 -1 O THR A 42 N ALA A 32 SHEET 3 AA1 9 ARG A 159 VAL A 163 -1 O ARG A 159 N GLN A 45 SHEET 4 AA1 9 GLY A 146 ILE A 152 -1 N GLY A 149 O VAL A 162 SHEET 5 AA1 9 TYR A 131 PRO A 137 -1 N LEU A 133 O ILE A 148 SHEET 6 AA1 9 VAL A 170 LYS A 175 -1 O VAL A 171 N TYR A 131 SHEET 7 AA1 9 GLY A 15 SER A 21 -1 N LEU A 20 O GLN A 172 SHEET 8 AA1 9 GLY A 55 SER A 59 -1 O THR A 56 N TYR A 17 SHEET 9 AA1 9 SER A 74 PHE A 77 -1 O LYS A 76 N ILE A 57 SHEET 1 AA2 6 ILE A 29 ALA A 32 0 SHEET 2 AA2 6 THR A 42 GLN A 45 -1 O THR A 42 N ALA A 32 SHEET 3 AA2 6 ARG A 159 VAL A 163 -1 O ARG A 159 N GLN A 45 SHEET 4 AA2 6 GLY A 146 ILE A 152 -1 N GLY A 149 O VAL A 162 SHEET 5 AA2 6 TYR A 131 PRO A 137 -1 N LEU A 133 O ILE A 148 SHEET 6 AA2 6 GLY A 116 ARG A 122 -1 N TRP A 117 O CYS A 136 SHEET 1 AA3 2 SER A 94 VAL A 96 0 SHEET 2 AA3 2 ALA A 104 LYS A 106 -1 O ALA A 104 N VAL A 96 SHEET 1 AA4 6 SER B 74 PHE B 77 0 SHEET 2 AA4 6 THR B 56 SER B 59 -1 N ILE B 57 O LYS B 76 SHEET 3 AA4 6 GLY B 15 SER B 21 -1 N TYR B 17 O THR B 56 SHEET 4 AA4 6 VAL B 170 LYS B 175 -1 O GLN B 172 N LEU B 20 SHEET 5 AA4 6 TYR B 131 PRO B 137 -1 N TYR B 131 O VAL B 171 SHEET 6 AA4 6 GLY B 116 ARG B 122 -1 N TRP B 117 O CYS B 136 SHEET 1 AA5 7 SER B 74 PHE B 77 0 SHEET 2 AA5 7 THR B 56 SER B 59 -1 N ILE B 57 O LYS B 76 SHEET 3 AA5 7 GLY B 15 SER B 21 -1 N TYR B 17 O THR B 56 SHEET 4 AA5 7 VAL B 170 LYS B 175 -1 O GLN B 172 N LEU B 20 SHEET 5 AA5 7 TYR B 131 PRO B 137 -1 N TYR B 131 O VAL B 171 SHEET 6 AA5 7 GLY B 146 ILE B 152 -1 O ILE B 148 N LEU B 133 SHEET 7 AA5 7 ARG B 159 VAL B 163 -1 O VAL B 162 N GLY B 149 SHEET 1 AA6 2 ILE B 29 ALA B 32 0 SHEET 2 AA6 2 THR B 42 GLN B 45 -1 O THR B 42 N ALA B 32 SHEET 1 AA7 2 SER B 94 VAL B 96 0 SHEET 2 AA7 2 ALA B 104 LYS B 106 -1 O ALA B 104 N VAL B 96 SSBOND 1 CYS A 39 CYS A 86 1555 1555 2.01 SSBOND 2 CYS A 136 CYS A 145 1555 1555 2.03 SSBOND 3 CYS B 39 CYS B 86 1555 1555 2.03 SSBOND 4 CYS B 136 CYS B 145 1555 1555 2.06 SITE 1 AC1 15 ARG A 30 SER A 46 ARG A 47 ASN A 48 SITE 2 AC1 15 ASP A 51 HOH A 301 HOH A 302 HOH A 303 SITE 3 AC1 15 HOH A 304 HOH A 305 HOH A 306 HOH A 307 SITE 4 AC1 15 HOH A 308 ASN B 48 21D B 201 SITE 1 AC2 9 ILE A 23 GLN A 45 ILE A 150 ARG A 159 SITE 2 AC2 9 PRO A 168 LEU A 169 VAL A 170 HOH A 312 SITE 3 AC2 9 HOH A 322 SITE 1 AC3 16 ASN A 48 21D A 201 HOH A 306 HOH A 308 SITE 2 AC3 16 ARG B 30 SER B 46 ARG B 47 ASN B 48 SITE 3 AC3 16 ASP B 51 HOH B 301 HOH B 302 HOH B 303 SITE 4 AC3 16 HOH B 304 HOH B 307 HOH B 312 HOH B 320 SITE 1 AC4 8 GLU B 37 ARG B 38 CYS B 39 LEU B 41 SITE 2 AC4 8 ILE B 89 PRO B 90 GLY B 108 GLU B 109 SITE 1 AC5 4 ILE B 64 ARG B 65 HOH B 339 HOH B 368 SITE 1 AC6 3 LYS B 76 PRO B 90 GLU B 92 SITE 1 AC7 8 TYR B 18 ILE B 19 LEU B 20 SER B 21 SITE 2 AC7 8 ASP B 22 ASN B 130 VAL B 171 PHE B 173 CRYST1 41.880 64.680 69.080 90.00 97.52 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 0.023878 0.000000 0.003152 0.00000 SCALE2 0.000000 0.015461 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014602 0.00000