HEADER IMMUNE SYSTEM 27-FEB-08 3CDY TITLE AL-09 H87Y, IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN LIGHT CHAIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KI O18/O8 GERMLINE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET12A KEYWDS GREEK KEY BETA BARREL, IMMUNOGLOBULIN, LIGHT CHAIN, VARIABLE DOMAIN, KEYWDS 2 AMYLOIDOSIS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR E.M.BADEN,E.G.RANDLES,A.K.ABOAGYE,J.R.THOMPSON,M.RAMIREZ-ALVARADO REVDAT 6 30-AUG-23 3CDY 1 REMARK REVDAT 5 13-JUL-11 3CDY 1 VERSN REVDAT 4 09-JUN-09 3CDY 1 REVDAT REVDAT 3 24-FEB-09 3CDY 1 VERSN REVDAT 2 02-DEC-08 3CDY 1 JRNL REVDAT 1 02-SEP-08 3CDY 0 JRNL AUTH E.M.BADEN,E.G.RANDLES,A.K.ABOAGYE,J.R.THOMPSON, JRNL AUTH 2 M.RAMIREZ-ALVARADO JRNL TITL STRUCTURAL INSIGHTS INTO THE ROLE OF MUTATIONS IN JRNL TITL 2 AMYLOIDOGENESIS. JRNL REF J.BIOL.CHEM. V. 283 30950 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18768467 JRNL DOI 10.1074/JBC.M804822200 REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 9593 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 494 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) : 2.43 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 706 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1676 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 57.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51000 REMARK 3 B22 (A**2) : 0.51000 REMARK 3 B33 (A**2) : -0.77000 REMARK 3 B12 (A**2) : 0.26000 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): 0.413 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.290 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.235 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.941 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1737 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1482 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2371 ; 1.789 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3491 ; 0.913 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 220 ; 7.739 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;40.351 ;25.584 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 281 ;19.261 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;17.555 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 265 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1958 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 333 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 276 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1507 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 791 ; 0.188 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1079 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 76 ; 0.189 ; 0.200 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): 8 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 37 ; 0.207 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.404 ; 0.200 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): 1396 ; 0.870 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 445 ; 0.157 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1776 ; 1.169 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 774 ; 1.876 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 594 ; 2.770 ; 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 : 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 107 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6134 -28.7354 12.8864 REMARK 3 T TENSOR REMARK 3 T11: -0.2116 T22: 0.0530 REMARK 3 T33: -0.1363 T12: -0.0263 REMARK 3 T13: 0.0136 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 4.2037 L22: 2.1538 REMARK 3 L33: 4.8424 L12: 1.5115 REMARK 3 L13: 1.2188 L23: -0.4128 REMARK 3 S TENSOR REMARK 3 S11: -0.0909 S12: -0.2117 S13: 0.0154 REMARK 3 S21: -0.0291 S22: 0.1545 S23: 0.0689 REMARK 3 S31: -0.0828 S32: -0.8563 S33: -0.0635 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 0 B 107 REMARK 3 ORIGIN FOR THE GROUP (A): 39.3192 -23.4928 9.5126 REMARK 3 T TENSOR REMARK 3 T11: -0.1567 T22: -0.0104 REMARK 3 T33: -0.1198 T12: -0.0861 REMARK 3 T13: -0.0013 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 3.9699 L22: 1.2855 REMARK 3 L33: 6.1755 L12: 0.6834 REMARK 3 L13: 1.5984 L23: -0.3937 REMARK 3 S TENSOR REMARK 3 S11: -0.2520 S12: 0.4714 S13: -0.0127 REMARK 3 S21: 0.0474 S22: 0.0369 S23: -0.0814 REMARK 3 S31: -0.4640 S32: 0.8772 S33: 0.2152 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 REMARK 4 REMARK 4 3CDY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979508 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : SI MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10539 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 64.061 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10100 REMARK 200 FOR THE DATA SET : 39.3800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36500 REMARK 200 FOR SHELL : 7.860 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: 2Q20 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% W/V POLYETHYLENE GLYCOL 4000 AND REMARK 280 0.2 M LI2SO4 IN 0.1 M TRIS BUFFER, PH 8.3, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 31.69000 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 63.38000 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 47.53500 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 79.22500 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 15.84500 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: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A -1 REMARK 465 SER B -1 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 B 130 O HOH B 136 1.71 REMARK 500 OG1 THR A 69 O HOH A 148 2.14 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 152 O HOH B 135 5554 1.87 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 LEU B 46 CA - CB - CG ANGL. DEV. = 15.0 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 ASN A 30 -125.66 57.80 REMARK 500 ALA A 51 -36.67 67.92 REMARK 500 ASN B 30 -120.13 59.18 REMARK 500 ALA B 51 -35.55 77.73 REMARK 500 SER B 52 -1.76 -151.64 REMARK 500 LEU B 83 107.41 -52.96 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 THR A 0 ASP A 1 149.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CDC RELATED DB: PDB REMARK 900 KI O18/O8 N34I/Y87H IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN REMARK 900 RELATED ID: 3CDF RELATED DB: PDB REMARK 900 KI O18/O8 Y87H IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN DBREF 3CDY A -1 107 PDB 3CDY 3CDY -1 107 DBREF 3CDY B -1 107 PDB 3CDY 3CDY -1 107 SEQRES 1 A 109 SER THR ASP ILE GLN MET THR GLN SER PRO SER SER LEU SEQRES 2 A 109 SER ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN SEQRES 3 A 109 ALA SER GLN ASP ILE ASN ASN TYR LEU ILE TRP TYR GLN SEQRES 4 A 109 GLN LYS PRO GLY GLN ALA PRO LYS LEU LEU ILE TYR ASP SEQRES 5 A 109 ALA SER THR LEU GLU THR GLY VAL PRO SER ARG PHE SER SEQRES 6 A 109 GLY SER GLY SER GLY THR GLU PHE THR PHE THR ILE SER SEQRES 7 A 109 SER LEU GLN PRO GLU ASP LEU ALA THR TYR TYR CYS GLN SEQRES 8 A 109 GLN TYR ASP ASN LEU PRO TYR THR PHE GLY GLN GLY THR SEQRES 9 A 109 LYS LEU GLU ILE LYS SEQRES 1 B 109 SER THR ASP ILE GLN MET THR GLN SER PRO SER SER LEU SEQRES 2 B 109 SER ALA SER VAL GLY ASP ARG VAL THR ILE THR CYS GLN SEQRES 3 B 109 ALA SER GLN ASP ILE ASN ASN TYR LEU ILE TRP TYR GLN SEQRES 4 B 109 GLN LYS PRO GLY GLN ALA PRO LYS LEU LEU ILE TYR ASP SEQRES 5 B 109 ALA SER THR LEU GLU THR GLY VAL PRO SER ARG PHE SER SEQRES 6 B 109 GLY SER GLY SER GLY THR GLU PHE THR PHE THR ILE SER SEQRES 7 B 109 SER LEU GLN PRO GLU ASP LEU ALA THR TYR TYR CYS GLN SEQRES 8 B 109 GLN TYR ASP ASN LEU PRO TYR THR PHE GLY GLN GLY THR SEQRES 9 B 109 LYS LEU GLU ILE LYS FORMUL 3 HOH *88(H2 O) HELIX 1 1 GLN A 79 LEU A 83 5 5 HELIX 2 2 GLN B 79 LEU B 83 5 5 SHEET 1 A 4 MET A 4 SER A 7 0 SHEET 2 A 4 VAL A 19 ALA A 25 -1 O GLN A 24 N THR A 5 SHEET 3 A 4 GLU A 70 ILE A 75 -1 O PHE A 73 N ILE A 21 SHEET 4 A 4 PHE A 62 SER A 67 -1 N SER A 65 O THR A 72 SHEET 1 B 6 SER A 10 ALA A 13 0 SHEET 2 B 6 THR A 102 ILE A 106 1 O GLU A 105 N LEU A 11 SHEET 3 B 6 THR A 85 GLN A 90 -1 N TYR A 86 O THR A 102 SHEET 4 B 6 LEU A 33 GLN A 38 -1 N GLN A 38 O THR A 85 SHEET 5 B 6 PRO A 44 TYR A 49 -1 O LEU A 47 N TRP A 35 SHEET 6 B 6 THR A 53 LEU A 54 -1 O THR A 53 N TYR A 49 SHEET 1 C 4 MET B 4 SER B 7 0 SHEET 2 C 4 VAL B 19 ALA B 25 -1 O THR B 22 N SER B 7 SHEET 3 C 4 GLU B 70 ILE B 75 -1 O PHE B 73 N ILE B 21 SHEET 4 C 4 PHE B 62 SER B 67 -1 N SER B 63 O THR B 74 SHEET 1 D 6 SER B 10 ALA B 13 0 SHEET 2 D 6 THR B 102 ILE B 106 1 O GLU B 105 N LEU B 11 SHEET 3 D 6 ALA B 84 GLN B 90 -1 N ALA B 84 O LEU B 104 SHEET 4 D 6 LEU B 33 GLN B 38 -1 N TYR B 36 O TYR B 87 SHEET 5 D 6 PRO B 44 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 D 6 THR B 53 LEU B 54 -1 O THR B 53 N TYR B 49 SHEET 1 E 4 SER B 10 ALA B 13 0 SHEET 2 E 4 THR B 102 ILE B 106 1 O GLU B 105 N LEU B 11 SHEET 3 E 4 ALA B 84 GLN B 90 -1 N ALA B 84 O LEU B 104 SHEET 4 E 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SSBOND 1 CYS A 23 CYS A 88 1555 1555 2.03 SSBOND 2 CYS B 23 CYS B 88 1555 1555 2.14 CISPEP 1 SER A 7 PRO A 8 0 0.80 CISPEP 2 LEU A 94 PRO A 95 0 -2.93 CISPEP 3 SER B 7 PRO B 8 0 -3.78 CISPEP 4 LEU B 94 PRO B 95 0 1.32 CRYST1 73.971 73.971 95.070 90.00 90.00 120.00 P 61 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 0.013519 0.007805 0.000000 0.00000 SCALE2 0.000000 0.015610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010519 0.00000