HEADER IMMUNE SYSTEM 23-NOV-19 6LDV TITLE STRUCTURE ANTIBODY F9 IN COMPLEX WITH METHYLATED PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FAB HEAVY CHAIN; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FAB LIGHT CHAIN; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: GLY-M3L-GLY-GLY-THR-TYR-PRO; COMPND 11 CHAIN: P; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_TAXID: 9986; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: 293; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 9 ORGANISM_TAXID: 9986; SOURCE 10 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM_CELL: 293; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_TAXID: 9606 KEYWDS METHYLATION, ANTIBODY, PHAGE DISPLAY, BIOMOLECULAR RECOGNITION, KEYWDS 2 IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,K.TSUMOTO REVDAT 4 22-NOV-23 6LDV 1 REMARK REVDAT 3 14-JUL-21 6LDV 1 JRNL REVDAT 2 23-DEC-20 6LDV 1 JRNL REVDAT 1 25-NOV-20 6LDV 0 JRNL AUTH M.ISHII,M.NAKAKIDO,J.M.M.CAAVEIRO,D.KURODA,C.J.OKUMURA, JRNL AUTH 2 T.MARUYAMA,K.ENTZMINGER,K.TSUMOTO JRNL TITL STRUCTURAL BASIS FOR ANTIGEN RECOGNITION BY METHYLATED JRNL TITL 2 LYSINE-SPECIFIC ANTIBODIES. JRNL REF J.BIOL.CHEM. V. 296 00176 2020 JRNL REFN ESSN 1083-351X JRNL PMID 33303630 JRNL DOI 10.1074/JBC.RA120.015996 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 30528 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1293 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1960 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3138 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 375 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : -0.69000 REMARK 3 B33 (A**2) : 1.41000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.033 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3242 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2873 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4452 ; 1.529 ; 1.658 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6708 ; 1.347 ; 1.563 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 427 ; 7.643 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;37.327 ;23.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 465 ;13.531 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;18.791 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 457 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3641 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 640 ; 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 : NULL 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REMARK 3 REFINED INDIVIDUALLY REMARK 3 REMARK 3 SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS REMARK 3 COLUMNS. REMARK 4 REMARK 4 6LDV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-18 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 : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31867 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 14.40 REMARK 200 R MERGE (I) : 0.19300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 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) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.21300 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: 5M63 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM IODIDE 20% PEG3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.76300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.92800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.76300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 62.92800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, P 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH H 454 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 530 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 542 LIES ON A SPECIAL POSITION. 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 CYS H 129 REMARK 465 GLY H 130 REMARK 465 ASP H 131 REMARK 465 THR H 132 REMARK 465 SER H 187 REMARK 465 SER H 188 REMARK 465 SER H 189 REMARK 465 GLN H 190 REMARK 465 SER H 212 REMARK 465 THR H 213 REMARK 465 CYS H 214 REMARK 465 SER H 215 REMARK 465 LYS H 216 REMARK 465 PRO H 217 REMARK 465 ALA H 218 REMARK 465 ALA H 219 REMARK 465 ALA H 220 REMARK 465 GLU H 221 REMARK 465 GLN H 222 REMARK 465 LYS H 223 REMARK 465 LEU H 224 REMARK 465 ILE H 225 REMARK 465 SER H 226 REMARK 465 GLU H 227 REMARK 465 GLU H 228 REMARK 465 ASP H 229 REMARK 465 LEU H 230 REMARK 465 ASN H 231 REMARK 465 SER H 232 REMARK 465 ALA H 233 REMARK 465 VAL H 234 REMARK 465 ASP H 235 REMARK 465 HIS H 236 REMARK 465 HIS H 237 REMARK 465 HIS H 238 REMARK 465 HIS H 239 REMARK 465 HIS H 240 REMARK 465 HIS H 241 REMARK 465 CYS L 215 REMARK 465 ALA L 216 REMARK 465 ALA L 217 REMARK 465 ALA L 218 REMARK 465 GLU L 219 REMARK 465 GLN L 220 REMARK 465 LYS L 221 REMARK 465 LEU L 222 REMARK 465 ILE L 223 REMARK 465 SER L 224 REMARK 465 GLU L 225 REMARK 465 GLU L 226 REMARK 465 ASP L 227 REMARK 465 LEU L 228 REMARK 465 ASN L 229 REMARK 465 SER L 230 REMARK 465 ALA L 231 REMARK 465 VAL L 232 REMARK 465 ASP L 233 REMARK 465 HIS L 234 REMARK 465 HIS L 235 REMARK 465 HIS L 236 REMARK 465 HIS L 237 REMARK 465 HIS L 238 REMARK 465 HIS L 239 REMARK 465 ASN P 1 REMARK 465 PRO P 2 REMARK 465 ILE P 3 REMARK 465 PHE P 4 REMARK 465 GLU P 5 REMARK 465 LYS P 6 REMARK 465 PHE P 7 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 H 510 O HOH H 544 2.19 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 H 496 O HOH L 455 1455 2.07 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 THR H 71 -164.23 -116.19 REMARK 500 LEU L 15 128.16 -39.03 REMARK 500 ASN L 32 -0.60 64.09 REMARK 500 ALA L 53 -40.96 73.48 REMARK 500 LYS L 142 76.28 46.45 REMARK 500 CYS L 174 -4.68 76.79 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 IOD H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD H 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD L 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD L 303 DBREF 6LDV H 1 241 PDB 6LDV 6LDV 1 241 DBREF 6LDV L 1 239 PDB 6LDV 6LDV 1 239 DBREF 6LDV P 1 14 PDB 6LDV 6LDV 1 14 SEQRES 1 H 241 GLN SER VAL GLU GLU SER GLY GLY ARG LEU VAL THR PRO SEQRES 2 H 241 GLY THR PRO LEU THR LEU THR CYS THR VAL SER GLY PHE SEQRES 3 H 241 SER LEU ASN SER ASN ALA ILE SER TRP VAL ARG GLN ALA SEQRES 4 H 241 PRO GLY GLU GLY LEU GLU TRP VAL GLY ALA ILE TYR THR SEQRES 5 H 241 HIS GLY SER THR VAL TYR ALA ASN TRP ALA LYS GLY ARG SEQRES 6 H 241 PHE THR ILE SER LYS THR SER THR THR ILE GLU LEU LYS SEQRES 7 H 241 MET THR SER LEU THR THR GLU ASP THR ALA THR TYR PHE SEQRES 8 H 241 CYS ALA ARG HIS GLY TYR THR TYR SER PHE ASN LEU TRP SEQRES 9 H 241 GLY PRO GLY THR LEU VAL THR VAL SER SER GLY GLN PRO SEQRES 10 H 241 LYS ALA PRO SER VAL PHE PRO LEU ALA PRO CYS CYS GLY SEQRES 11 H 241 ASP THR PRO SER SER THR VAL THR LEU GLY CYS LEU VAL SEQRES 12 H 241 LYS GLY TYR LEU PRO GLU PRO VAL THR VAL THR TRP ASN SEQRES 13 H 241 SER GLY THR LEU THR ASN GLY VAL ARG THR PHE PRO SER SEQRES 14 H 241 VAL ARG GLN SER SER GLY LEU TYR SER LEU SER SER VAL SEQRES 15 H 241 VAL SER VAL THR SER SER SER GLN PRO VAL THR CYS ASN SEQRES 16 H 241 VAL ALA HIS PRO ALA THR ASN THR LYS VAL ASP LYS THR SEQRES 17 H 241 VAL ALA PRO SER THR CYS SER LYS PRO ALA ALA ALA GLU SEQRES 18 H 241 GLN LYS LEU ILE SER GLU GLU ASP LEU ASN SER ALA VAL SEQRES 19 H 241 ASP HIS HIS HIS HIS HIS HIS SEQRES 1 L 239 ALA GLN GLY LEU THR GLN THR PRO SER PRO VAL SER ALA SEQRES 2 L 239 ALA LEU GLY GLY THR VAL THR ILE ASN CYS GLN SER SER SEQRES 3 L 239 GLN SER VAL TYR GLY ASN ASN ARG LEU ALA TRP TYR GLN SEQRES 4 L 239 GLN LYS PRO GLY GLN PRO PRO LYS ARG LEU ILE TYR GLN SEQRES 5 L 239 ALA SER THR LEU ASP SER GLY VAL PRO SER ARG PHE SER SEQRES 6 L 239 GLY SER GLY SER GLY THR GLN PHE THR LEU THR ILE SER SEQRES 7 L 239 GLY VAL GLN CYS ASP ASP ALA ALA THR TYR TYR CYS GLN SEQRES 8 L 239 GLY GLY TYR SER SER GLY ASP ALA TRP ALA PHE GLY GLY SEQRES 9 L 239 GLY THR GLU VAL VAL VAL LYS GLY ASP PRO VAL ALA PRO SEQRES 10 L 239 THR VAL LEU ILE PHE PRO PRO SER ALA ASP LEU VAL ALA SEQRES 11 L 239 THR GLY THR VAL THR ILE VAL CYS VAL ALA ASN LYS TYR SEQRES 12 L 239 PHE PRO ASP VAL THR VAL THR TRP GLU VAL ASP GLY THR SEQRES 13 L 239 THR GLN THR THR GLY ILE GLU ASN SER LYS THR PRO GLN SEQRES 14 L 239 ASN SER ALA ASP CYS THR TYR ASN LEU SER SER THR LEU SEQRES 15 L 239 THR LEU THR SER THR GLN TYR ASN SER HIS LYS GLU TYR SEQRES 16 L 239 THR CYS LYS VAL THR GLN GLY THR THR SER VAL VAL GLN SEQRES 17 L 239 SER PHE ASN ARG GLY ASP CYS ALA ALA ALA GLU GLN LYS SEQRES 18 L 239 LEU ILE SER GLU GLU ASP LEU ASN SER ALA VAL ASP HIS SEQRES 19 L 239 HIS HIS HIS HIS HIS SEQRES 1 P 14 ASN PRO ILE PHE GLU LYS PHE GLY M3L GLY GLY THR TYR SEQRES 2 P 14 PRO HET M3L P 9 12 HET IOD H 301 1 HET IOD H 302 1 HET IOD H 303 2 HET IOD H 304 1 HET IOD H 305 2 HET IOD L 301 2 HET IOD L 302 1 HET IOD L 303 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM IOD IODIDE ION FORMUL 3 M3L C9 H21 N2 O2 1+ FORMUL 4 IOD 8(I 1-) FORMUL 12 HOH *375(H2 O) HELIX 1 AA1 ASN H 60 LYS H 63 5 4 HELIX 2 AA2 THR H 83 THR H 87 5 5 HELIX 3 AA3 SER H 157 THR H 159 5 3 HELIX 4 AA4 PRO H 199 ASN H 202 5 4 HELIX 5 AA5 VAL L 29 ASN L 33 5 5 HELIX 6 AA6 GLN L 81 ALA L 85 5 5 HELIX 7 AA7 SER L 125 THR L 131 1 7 HELIX 8 AA8 SER L 186 SER L 191 1 6 SHEET 1 AA1 4 SER H 2 SER H 6 0 SHEET 2 AA1 4 LEU H 17 SER H 24 -1 O THR H 22 N GLU H 4 SHEET 3 AA1 4 THR H 74 MET H 79 -1 O ILE H 75 N CYS H 21 SHEET 4 AA1 4 PHE H 66 LYS H 70 -1 N THR H 67 O LYS H 78 SHEET 1 AA2 6 LEU H 10 VAL H 11 0 SHEET 2 AA2 6 THR H 108 VAL H 112 1 O THR H 111 N VAL H 11 SHEET 3 AA2 6 ALA H 88 HIS H 95 -1 N TYR H 90 O THR H 108 SHEET 4 AA2 6 ILE H 33 GLN H 38 -1 N VAL H 36 O PHE H 91 SHEET 5 AA2 6 GLU H 45 ILE H 50 -1 O VAL H 47 N TRP H 35 SHEET 6 AA2 6 THR H 56 TYR H 58 -1 O VAL H 57 N ALA H 49 SHEET 1 AA3 4 LEU H 10 VAL H 11 0 SHEET 2 AA3 4 THR H 108 VAL H 112 1 O THR H 111 N VAL H 11 SHEET 3 AA3 4 ALA H 88 HIS H 95 -1 N TYR H 90 O THR H 108 SHEET 4 AA3 4 PHE H 101 TRP H 104 -1 O ASN H 102 N ARG H 94 SHEET 1 AA4 4 SER H 121 LEU H 125 0 SHEET 2 AA4 4 VAL H 137 TYR H 146 -1 O GLY H 140 N LEU H 125 SHEET 3 AA4 4 TYR H 177 VAL H 185 -1 O LEU H 179 N VAL H 143 SHEET 4 AA4 4 ARG H 165 THR H 166 -1 N ARG H 165 O VAL H 182 SHEET 1 AA5 4 SER H 121 LEU H 125 0 SHEET 2 AA5 4 VAL H 137 TYR H 146 -1 O GLY H 140 N LEU H 125 SHEET 3 AA5 4 TYR H 177 VAL H 185 -1 O LEU H 179 N VAL H 143 SHEET 4 AA5 4 VAL H 170 ARG H 171 -1 N VAL H 170 O SER H 178 SHEET 1 AA6 3 THR H 152 TRP H 155 0 SHEET 2 AA6 3 VAL H 192 HIS H 198 -1 O ASN H 195 N THR H 154 SHEET 3 AA6 3 THR H 203 VAL H 209 -1 O VAL H 205 N VAL H 196 SHEET 1 AA7 4 LEU L 4 GLN L 6 0 SHEET 2 AA7 4 VAL L 19 SER L 25 -1 O GLN L 24 N THR L 5 SHEET 3 AA7 4 GLN L 72 ILE L 77 -1 O LEU L 75 N ILE L 21 SHEET 4 AA7 4 PHE L 64 SER L 69 -1 N SER L 65 O THR L 76 SHEET 1 AA8 6 VAL L 11 ALA L 14 0 SHEET 2 AA8 6 THR L 106 LYS L 111 1 O LYS L 111 N ALA L 13 SHEET 3 AA8 6 ALA L 86 GLY L 93 -1 N ALA L 86 O VAL L 108 SHEET 4 AA8 6 LEU L 35 GLN L 40 -1 N TYR L 38 O TYR L 89 SHEET 5 AA8 6 LYS L 47 TYR L 51 -1 O LEU L 49 N TRP L 37 SHEET 6 AA8 6 THR L 55 LEU L 56 -1 O THR L 55 N TYR L 51 SHEET 1 AA9 4 VAL L 11 ALA L 14 0 SHEET 2 AA9 4 THR L 106 LYS L 111 1 O LYS L 111 N ALA L 13 SHEET 3 AA9 4 ALA L 86 GLY L 93 -1 N ALA L 86 O VAL L 108 SHEET 4 AA9 4 TRP L 100 PHE L 102 -1 O ALA L 101 N GLY L 92 SHEET 1 AB1 4 THR L 118 PHE L 122 0 SHEET 2 AB1 4 THR L 133 TYR L 143 -1 O ASN L 141 N THR L 118 SHEET 3 AB1 4 TYR L 176 THR L 185 -1 O LEU L 184 N VAL L 134 SHEET 4 AB1 4 ILE L 162 LYS L 166 -1 N SER L 165 O SER L 179 SHEET 1 AB2 4 THR L 156 GLN L 158 0 SHEET 2 AB2 4 THR L 148 VAL L 153 -1 N TRP L 151 O GLN L 158 SHEET 3 AB2 4 GLU L 194 GLN L 201 -1 O LYS L 198 N THR L 150 SHEET 4 AB2 4 THR L 204 ASN L 211 -1 O VAL L 206 N VAL L 199 SSBOND 1 CYS H 21 CYS H 92 1555 1555 2.07 SSBOND 2 CYS H 141 CYS H 194 1555 1555 2.00 SSBOND 3 CYS L 23 CYS L 90 1555 1555 2.13 SSBOND 4 CYS L 82 CYS L 174 1555 1555 2.06 SSBOND 5 CYS L 138 CYS L 197 1555 1555 2.00 LINK C GLY P 8 N M3L P 9 1555 1555 1.34 LINK C M3L P 9 N GLY P 10 1555 1555 1.34 CISPEP 1 LEU H 147 PRO H 148 0 -12.25 CISPEP 2 GLU H 149 PRO H 150 0 -6.09 CISPEP 3 SER L 9 PRO L 10 0 -10.96 CISPEP 4 PHE L 144 PRO L 145 0 2.82 SITE 1 AC1 2 ARG H 9 LEU H 10 SITE 1 AC2 3 SER H 30 ASN H 31 THR P 12 SITE 1 AC3 3 LYS H 144 GLY H 145 GLN H 172 SITE 1 AC4 3 LYS H 118 GLY H 145 HOH L 555 SITE 1 AC5 2 ALA L 14 HOH L 475 SITE 1 AC6 1 ARG H 165 SITE 1 AC7 1 LYS L 111 CRYST1 49.764 63.526 125.856 90.00 90.00 90.00 P 2 21 21 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 0.020095 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007946 0.00000