PDB Short entry for 3KYK HEADER IMMUNE SYSTEM 06-DEC-09 3KYK TITLE CRYSTAL STRUCTURE OF LI33 IGG1 FAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN LI33 IGG1; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN LI33 IGG1; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HEAVY CHAIN LI33; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: LIGHT CHAIN LI33; SOURCE 13 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS ANTIBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.F.SILVIAN,R.B.PEPINSKY,L.WALUS REVDAT 4 06-SEP-23 3KYK 1 REMARK REVDAT 3 01-NOV-17 3KYK 1 REMARK REVDAT 2 19-MAY-10 3KYK 1 JRNL REVDAT 1 16-MAR-10 3KYK 0 JRNL AUTH R.B.PEPINSKY,L.SILVIAN,S.A.BERKOWITZ,G.FARRINGTON, JRNL AUTH 2 A.LUGOVSKOY,L.WALUS,J.ELDREDGE,A.CAPILI,S.MI,C.GRAFF, JRNL AUTH 3 E.GARBER JRNL TITL IMPROVING THE SOLUBILITY OF ANTI-LINGO-1 MONOCLONAL ANTIBODY JRNL TITL 2 LI33 BY ISOTYPE SWITCHING AND TARGETED MUTAGENESIS. JRNL REF PROTEIN SCI. V. 19 954 2010 JRNL REFN ISSN 0961-8368 JRNL PMID 20198683 JRNL DOI 10.1002/PRO.372 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9257 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 442 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 621 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.4550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3251 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.16000 REMARK 3 B12 (A**2) : -0.05000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.577 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.236 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.100 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.812 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3349 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4562 ; 2.381 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 8.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;34.146 ;24.122 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 512 ;23.627 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;24.045 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 505 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2518 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2133 ; 0.741 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3433 ; 1.451 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1216 ; 2.109 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1129 ; 3.555 ; 4.500 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 : 1.40 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 3KYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 93.0 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97961 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9258 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.80 REMARK 200 R MERGE (I) : 0.22100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 17.20 REMARK 200 R MERGE FOR SHELL (I) : 0.57100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.3.2 REMARK 200 STARTING MODEL: PDB ENTRY 2B2X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE PH 3.5 AND 0.1M TCEP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 143.36067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.68033 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 107.52050 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.84017 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 179.20083 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 143.36067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 71.68033 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 35.84017 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 107.52050 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 179.20083 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L 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 SER H 221 REMARK 465 CYS H 222 REMARK 465 ASP H 223 REMARK 465 LYS H 224 REMARK 465 THR H 225 REMARK 465 HIS H 226 REMARK 465 THR H 227 REMARK 465 GLY L 212 REMARK 465 GLU L 213 REMARK 465 CYS L 214 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU H 5 O REMARK 470 GLY H 9 O REMARK 470 PRO H 14 O REMARK 470 TYR H 32 O REMARK 470 PRO H 33 O REMARK 470 VAL H 37 O REMARK 470 ARG H 111 CG CD NE CZ NH1 NH2 REMARK 470 LYS H 215 CG CD CE NZ REMARK 470 LYS H 216 CG CD CE NZ REMARK 470 LYS H 220 CG CD CE NZ REMARK 470 LYS L 93 CG CD CE NZ REMARK 470 LYS L 188 CG CD CE NZ REMARK 470 THR L 206 CG2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS H 215 CB REMARK 480 LYS H 216 CB REMARK 480 LYS H 220 CB 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 NH1 ARG L 18 O HOH L 217 2.11 REMARK 500 OG SER H 134 O HOH H 232 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 NE2 HIS H 101 NE2 HIS H 101 10555 0.89 REMARK 500 CD2 HIS H 101 CD2 HIS H 101 10555 1.13 REMARK 500 CD2 HIS H 101 NE2 HIS H 101 10555 1.47 REMARK 500 CE1 HIS H 101 NE2 HIS H 101 10555 2.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS H 96 CB CYS H 96 SG -0.184 REMARK 500 GLN L 3 CG GLN L 3 CD 0.140 REMARK 500 GLU L 17 CB GLU L 17 CG 0.172 REMARK 500 GLU L 17 CG GLU L 17 CD 0.170 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS H 96 CA - CB - SG ANGL. DEV. = -12.8 DEGREES REMARK 500 ASP H 103 N - CA - C ANGL. DEV. = -23.3 DEGREES REMARK 500 LYS H 215 CB - CA - C ANGL. DEV. = 13.5 DEGREES REMARK 500 ASP L 50 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 TYR L 91 N - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 PRO L 120 C - N - CA ANGL. DEV. = 16.0 DEGREES REMARK 500 PRO L 120 C - N - CD ANGL. DEV. = -14.7 DEGREES 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 GLN H 13 141.29 -39.32 REMARK 500 LEU H 18 149.52 -170.54 REMARK 500 GLN H 39 110.04 -166.01 REMARK 500 SER H 54 -36.62 -38.37 REMARK 500 TRP H 104 -5.18 110.52 REMARK 500 GLN H 177 138.40 -35.85 REMARK 500 SER H 179 -74.44 -37.51 REMARK 500 PRO H 191 113.07 -33.23 REMARK 500 THR H 197 -77.47 -69.59 REMARK 500 ASN H 210 97.24 -68.05 REMARK 500 SER L 7 -70.75 -63.21 REMARK 500 SER L 30 -126.78 54.85 REMARK 500 PRO L 44 138.86 -37.17 REMARK 500 ALA L 51 -59.74 70.60 REMARK 500 LEU L 78 150.26 -47.48 REMARK 500 TYR L 91 26.73 44.72 REMARK 500 SER L 121 -1.64 106.18 REMARK 500 ASP L 122 -70.89 87.11 REMARK 500 ASN L 138 61.87 72.43 REMARK 500 ASN L 152 8.28 54.19 REMARK 500 LYS L 169 -78.39 -74.71 REMARK 500 SER L 171 12.76 53.82 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 PRO L 40 GLY L 41 -35.11 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 SO4 H 228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 229 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 H 230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 L 215 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KYM RELATED DB: PDB DBREF 3KYK H 1 227 PDB 3KYK 3KYK 1 227 DBREF 3KYK L 1 214 PDB 3KYK 3KYK 1 214 SEQRES 1 H 227 GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 227 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 227 PHE THR PHE SER ILE TYR PRO MET PHE TRP VAL ARG GLN SEQRES 4 H 227 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER TRP ILE GLY SEQRES 5 H 227 PRO SER GLY GLY ILE THR LYS TYR ALA ASP SER VAL LYS SEQRES 6 H 227 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 227 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 227 ALA THR TYR TYR CYS ALA ARG GLU GLY HIS ASN ASP TRP SEQRES 9 H 227 TYR PHE ASP LEU TRP GLY ARG GLY THR LEU VAL THR VAL SEQRES 10 H 227 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 H 227 ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA SEQRES 12 H 227 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 H 227 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 H 227 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 H 227 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 H 227 GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SEQRES 17 H 227 SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER SEQRES 18 H 227 CYS ASP LYS THR HIS THR SEQRES 1 L 214 ASP ILE GLN MET THR GLN SER PRO GLY THR LEU SER LEU SEQRES 2 L 214 SER PRO GLY GLU ARG ALA THR LEU SER CYS ARG ALA SER SEQRES 3 L 214 GLN SER VAL SER SER TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 L 214 PRO GLY GLN ALA PRO ARG LEU LEU ILE TYR ASP ALA SER SEQRES 5 L 214 ASN ARG ALA THR GLY ILE PRO ALA ARG PHE SER GLY SER SEQRES 6 L 214 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 L 214 GLN SER GLU ASP PHE ALA VAL TYR TYR CYS GLN GLN TYR SEQRES 8 L 214 ASP LYS TRP PRO LEU THR PHE GLY GLY GLY THR LYS VAL SEQRES 9 L 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 L 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 L 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 L 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 L 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 L 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 L 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 L 214 PHE ASN ARG GLY GLU CYS HET SO4 H 228 5 HET SO4 H 229 5 HET SO4 H 230 5 HET SO4 L 215 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 HOH *38(H2 O) HELIX 1 1 THR H 28 TYR H 32 5 5 HELIX 2 2 ARG H 87 THR H 91 5 5 HELIX 3 3 SER H 133 LYS H 135 5 3 HELIX 4 4 SER H 162 ALA H 164 5 3 HELIX 5 5 SER H 193 GLY H 196 5 4 HELIX 6 6 GLN L 79 PHE L 83 5 5 HELIX 7 7 ASP L 122 SER L 127 1 6 HELIX 8 8 LYS L 183 GLU L 187 1 5 SHEET 1 A 3 LEU H 18 SER H 21 0 SHEET 2 A 3 THR H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 3 A 3 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 B 5 THR H 58 TYR H 60 0 SHEET 2 B 5 SER H 49 ILE H 51 -1 N TRP H 50 O LYS H 59 SHEET 3 B 5 PHE H 35 TRP H 36 -1 N TRP H 36 O SER H 49 SHEET 4 B 5 CYS H 96 GLU H 99 -1 O ALA H 97 N PHE H 35 SHEET 5 B 5 PHE H 106 TRP H 109 -1 O LEU H 108 N ARG H 98 SHEET 1 C 2 ALA H 92 TYR H 94 0 SHEET 2 C 2 THR H 113 VAL H 115 -1 O THR H 113 N TYR H 94 SHEET 1 D 4 SER H 126 LEU H 130 0 SHEET 2 D 4 THR H 141 TYR H 151 -1 O LYS H 149 N SER H 126 SHEET 3 D 4 TYR H 182 PRO H 191 -1 O LEU H 184 N VAL H 148 SHEET 4 D 4 VAL H 169 THR H 171 -1 N HIS H 170 O VAL H 187 SHEET 1 E 4 THR H 137 SER H 138 0 SHEET 2 E 4 THR H 141 TYR H 151 -1 O THR H 141 N SER H 138 SHEET 3 E 4 TYR H 182 PRO H 191 -1 O LEU H 184 N VAL H 148 SHEET 4 E 4 VAL H 175 LEU H 176 -1 N VAL H 175 O SER H 183 SHEET 1 F 3 THR H 157 TRP H 160 0 SHEET 2 F 3 TYR H 200 HIS H 206 -1 O ASN H 203 N SER H 159 SHEET 3 F 3 THR H 211 VAL H 217 -1 O VAL H 217 N TYR H 200 SHEET 1 G 4 MET L 4 GLN L 6 0 SHEET 2 G 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 G 4 GLU L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 G 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 H 6 THR L 10 LEU L 13 0 SHEET 2 H 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 H 6 ALA L 84 GLN L 89 -1 N TYR L 86 O THR L 102 SHEET 4 H 6 ALA L 34 GLN L 38 -1 N TYR L 36 O TYR L 87 SHEET 5 H 6 ARG L 45 TYR L 49 -1 O ARG L 45 N GLN L 37 SHEET 6 H 6 ASN L 53 ARG L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 I 4 SER L 114 PHE L 118 0 SHEET 2 I 4 THR L 129 PHE L 139 -1 O LEU L 135 N PHE L 116 SHEET 3 I 4 TYR L 173 SER L 182 -1 O LEU L 175 N LEU L 136 SHEET 4 I 4 SER L 162 VAL L 163 -1 N SER L 162 O SER L 176 SHEET 1 J 4 ALA L 153 LEU L 154 0 SHEET 2 J 4 LYS L 145 VAL L 150 -1 N VAL L 150 O ALA L 153 SHEET 3 J 4 TYR L 192 THR L 197 -1 O GLU L 195 N GLN L 147 SHEET 4 J 4 VAL L 205 LYS L 207 -1 O VAL L 205 N VAL L 196 SSBOND 1 CYS H 22 CYS H 96 1555 1555 1.99 SSBOND 2 CYS H 146 CYS H 202 1555 1555 2.03 SSBOND 3 CYS L 23 CYS L 88 1555 1555 2.11 SSBOND 4 CYS L 134 CYS L 194 1555 1555 2.14 CISPEP 1 ASN H 102 ASP H 103 0 -27.68 CISPEP 2 LYS H 149 ASP H 150 0 -24.22 CISPEP 3 PHE H 152 PRO H 153 0 8.45 CISPEP 4 TRP L 94 PRO L 95 0 -3.19 CISPEP 5 TYR L 140 PRO L 141 0 5.95 CISPEP 6 GLY L 157 ASN L 158 0 -14.97 SITE 1 AC1 7 TRP H 47 ALA H 61 ASP H 62 THR H 137 SITE 2 AC1 7 SER H 138 GLY H 139 ASP L 1 SITE 1 AC2 4 THR H 58 LYS H 59 TYR H 60 LYS H 65 SITE 1 AC3 4 ARG H 87 ALA H 88 GLU H 89 ARG L 108 SITE 1 AC4 4 ARG L 45 PRO L 59 ARG L 61 GLU L 81 CRYST1 90.632 90.632 215.041 90.00 90.00 120.00 P 65 2 2 12 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 0.011034 0.006370 0.000000 0.00000 SCALE2 0.000000 0.012741 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004650 0.00000