HEADER IMMUNE SYSTEM 08-NOV-13 4NJA TITLE CRYSTAL STRUCTURE OF FAB 6C8 IN COMPLEX WITH MPTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6C8 LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: 6C8 HEAVY CHAIN; COMPND 6 CHAIN: H SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 OTHER_DETAILS: HYBRIDOMA; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_COMMON: MOUSE, MOUSE; SOURCE 9 ORGANISM_TAXID: 10090; SOURCE 10 STRAIN: SWISS WEBSTER; SOURCE 11 OTHER_DETAILS: HYBRIDOMA KEYWDS IMMUNOGLOBULIN FOLD, MPTS BINDING, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.L.STANFIELD,F.E.ROMESBERG,J.ZIMMERMANN,I.A.WILSON REVDAT 5 20-SEP-23 4NJA 1 REMARK LINK REVDAT 4 21-JUN-17 4NJA 1 DBREF REVDAT 3 08-APR-15 4NJA 1 JRNL REVDAT 2 25-MAR-15 4NJA 1 ATOM DBREF JRNL REMARK REVDAT 2 2 1 SITE REVDAT 1 12-NOV-14 4NJA 0 JRNL AUTH R.ADHIKARY,W.YU,M.ODA,R.C.WALKER,T.CHEN,R.L.STANFIELD, JRNL AUTH 2 I.A.WILSON,J.ZIMMERMANN,F.E.ROMESBERG JRNL TITL ADAPTIVE MUTATIONS ALTER ANTIBODY STRUCTURE AND DYNAMICS JRNL TITL 2 DURING AFFINITY MATURATION. JRNL REF BIOCHEMISTRY V. 54 2085 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 25756188 JRNL DOI 10.1021/BI501417Q REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 27076 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1446 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1889 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3338 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66000 REMARK 3 B22 (A**2) : -2.98000 REMARK 3 B33 (A**2) : 3.64000 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): 0.255 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.174 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.686 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3468 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4733 ; 1.788 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 436 ; 8.391 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;32.842 ;24.191 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 538 ;18.054 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;19.521 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 520 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2627 ; 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): 1752 ; 1.273 ; 1.873 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2184 ; 1.942 ; 2.796 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1716 ; 1.864 ; 1.995 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 : 4 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 : L 1 L 111 REMARK 3 ORIGIN FOR THE GROUP (A): -35.7080 1.9680 13.1673 REMARK 3 T TENSOR REMARK 3 T11: 0.0409 T22: 0.0378 REMARK 3 T33: 0.0892 T12: 0.0085 REMARK 3 T13: 0.0460 T23: -0.0152 REMARK 3 L TENSOR REMARK 3 L11: 3.9185 L22: 10.1862 REMARK 3 L33: 3.1801 L12: -1.8452 REMARK 3 L13: -0.4078 L23: 1.5509 REMARK 3 S TENSOR REMARK 3 S11: 0.2357 S12: 0.0606 S13: 0.2267 REMARK 3 S21: 0.3447 S22: -0.1490 S23: 0.6741 REMARK 3 S31: 0.1403 S32: 0.1309 S33: -0.0867 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 : L 112 L 217 REMARK 3 ORIGIN FOR THE GROUP (A): -21.2377 36.9794 9.9173 REMARK 3 T TENSOR REMARK 3 T11: 0.2588 T22: 0.2469 REMARK 3 T33: 0.1063 T12: -0.0583 REMARK 3 T13: -0.0700 T23: 0.0759 REMARK 3 L TENSOR REMARK 3 L11: 7.2140 L22: 10.1345 REMARK 3 L33: 2.2002 L12: 7.0051 REMARK 3 L13: -2.4878 L23: -2.8243 REMARK 3 S TENSOR REMARK 3 S11: -0.2485 S12: 0.4579 S13: 0.3557 REMARK 3 S21: -0.2245 S22: 0.1676 S23: 0.2691 REMARK 3 S31: -0.1748 S32: 0.0265 S33: 0.0809 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 121 REMARK 3 ORIGIN FOR THE GROUP (A): -14.7874 -3.6896 13.2938 REMARK 3 T TENSOR REMARK 3 T11: 0.1597 T22: 0.2787 REMARK 3 T33: 0.3391 T12: 0.1558 REMARK 3 T13: -0.1493 T23: -0.1166 REMARK 3 L TENSOR REMARK 3 L11: 5.7328 L22: 4.7274 REMARK 3 L33: 2.9145 L12: 2.5390 REMARK 3 L13: -1.5377 L23: -0.5003 REMARK 3 S TENSOR REMARK 3 S11: 0.0770 S12: -0.0696 S13: -0.2435 REMARK 3 S21: 0.3843 S22: 0.1195 S23: -1.1538 REMARK 3 S31: 0.2512 S32: 0.5017 S33: -0.1965 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 122 H 221 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9514 29.7552 20.4267 REMARK 3 T TENSOR REMARK 3 T11: 0.3755 T22: 0.2605 REMARK 3 T33: 0.2477 T12: -0.0748 REMARK 3 T13: -0.2024 T23: 0.0801 REMARK 3 L TENSOR REMARK 3 L11: 3.7430 L22: 8.9083 REMARK 3 L33: 3.3491 L12: -0.1904 REMARK 3 L13: -0.9375 L23: 3.3955 REMARK 3 S TENSOR REMARK 3 S11: 0.1068 S12: -0.1686 S13: -0.2983 REMARK 3 S21: 0.8440 S22: -0.1819 S23: -1.0059 REMARK 3 S31: -0.0261 S32: 0.2055 S33: 0.0751 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4NJA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03318 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28547 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 42.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: PDB ENTRY 4NJ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM ZINC ACETATE, 12% PEG 8000, 0.1M REMARK 280 MES, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 46.33000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.91850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.33000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.91850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 4720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H 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 CYS L 214 REMARK 465 GLY H 227 REMARK 465 PRO H 228 REMARK 465 ILE H 229 REMARK 465 SER H 230 REMARK 465 THR H 231 REMARK 465 ILE H 232 REMARK 465 ASN H 233 REMARK 465 PRO H 234 REMARK 465 CYS H 235 REMARK 465 PRO H 236 REMARK 465 PRO H 237 REMARK 465 CYS H 238 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 SER H 74 CA SER H 74 CB 0.100 REMARK 500 SER H 74 CB SER H 74 OG 0.119 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 ARG H 95 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG H 95 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ALA L 51 -48.72 78.04 REMARK 500 ARG L 68 -95.08 58.04 REMARK 500 ASN L 76 111.56 -160.30 REMARK 500 ALA L 130 99.26 -165.89 REMARK 500 ASN L 157 -146.86 -108.89 REMARK 500 LYS H 43 -86.01 -120.59 REMARK 500 PRO H 52A -75.27 -68.97 REMARK 500 ASN H 53 -53.00 -29.71 REMARK 500 ASN H 54 -80.80 -85.44 REMARK 500 SER H 76 42.99 34.07 REMARK 500 SER H 167 -73.80 -153.68 REMARK 500 SER H 196 -4.77 -59.03 REMARK 500 SER H 216 14.83 57.26 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 ARG L 155 GLN L 156 142.57 REMARK 500 THR H 134 GLY H 135 -39.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN L 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 27 OE1 REMARK 620 2 GLU L 93 OE1 98.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN L 138 OD1 REMARK 620 2 HIS H 172 NE2 94.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN L 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT L 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT L 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2M9 H 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 H 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN H 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NJ9 RELATED DB: PDB REMARK 900 FAB 8B10 IN COMPLEX WITH MPTS DBREF 4NJA L 1 107 UNP P01660 KV3A8_MOUSE 1 111 DBREF 4NJA L 108 214 UNP Q52L95 Q52L95_MOUSE 130 236 DBREF 4NJA H 1 113 PDB 4NJA 4NJA 1 113 DBREF1 4NJA H 114 238 UNP A0A0F7R1P3_MOUSE DBREF2 4NJA H A0A0F7R1P3 134 245 SEQADV 4NJA ARG L 96 UNP P01660 TYR 100 CONFLICT SEQADV 4NJA SER H 140 UNP A0A0F7R1P LEU 158 CONFLICT SEQADV 4NJA PRO H 151 UNP A0A0F7R1P SER 169 CONFLICT SEQRES 1 L 218 ASP ILE VAL LEU THR GLN SER PRO ALA SER LEU ALA VAL SEQRES 2 L 218 SER LEU GLY GLN ARG ALA THR ILE SER CYS ARG ALA SER SEQRES 3 L 218 GLU SER VAL ASP SER TYR GLY ASN SER PHE MET HIS TRP SEQRES 4 L 218 TYR GLN GLN LYS PRO GLY GLN PRO PRO LYS LEU LEU ILE SEQRES 5 L 218 TYR ARG ALA SER ASN LEU GLU SER GLY ILE PRO ALA ARG SEQRES 6 L 218 PHE SER GLY SER GLY SER ARG THR ASP PHE THR LEU THR SEQRES 7 L 218 ILE ASN PRO VAL GLU ALA ASP ASP VAL ALA THR TYR TYR SEQRES 8 L 218 CYS GLN GLN SER ASN GLU ASP PRO ARG THR PHE GLY GLY SEQRES 9 L 218 GLY THR LYS LEU GLU ILE LYS ARG ALA ASP ALA ALA PRO SEQRES 10 L 218 THR VAL SER ILE PHE PRO PRO SER SER GLU GLN LEU THR SEQRES 11 L 218 SER GLY GLY ALA SER VAL VAL CYS PHE LEU ASN ASN PHE SEQRES 12 L 218 TYR PRO LYS ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SEQRES 13 L 218 SER GLU ARG GLN ASN GLY VAL LEU ASN SER TRP THR ASP SEQRES 14 L 218 GLN ASP SER LYS ASP SER THR TYR SER MET SER SER THR SEQRES 15 L 218 LEU THR LEU THR LYS ASP GLU TYR GLU ARG HIS ASN SER SEQRES 16 L 218 TYR THR CYS GLU ALA THR HIS LYS THR SER THR SER PRO SEQRES 17 L 218 ILE VAL LYS SER PHE ASN ARG ASN GLU CYS SEQRES 1 H 233 GLU VAL GLN LEU GLN GLN SER GLY PRO GLU LEU VAL LYS SEQRES 2 H 233 PRO GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 H 233 TYR THR PHE THR ASP TYR TYR MET HIS TRP VAL LYS GLN SEQRES 4 H 233 SER HIS GLY LYS SER LEU GLU TRP ILE GLY TYR ILE TYR SEQRES 5 H 233 PRO ASN ASN GLY GLY ASN GLY TYR ASN GLN LYS PHE LYS SEQRES 6 H 233 GLY LYS ALA THR LEU THR VAL ASP LYS SER SER SER THR SEQRES 7 H 233 ALA TYR MET GLU LEU ARG SER LEU THR SER ASP ASP SER SEQRES 8 H 233 ALA VAL TYR TYR CYS ALA ARG ARG GLY GLY TYR GLY ILE SEQRES 9 H 233 ARG GLY TYR PHE ASP VAL TRP GLY THR GLY THR THR VAL SEQRES 10 H 233 THR VAL SER SER ALA LYS THR THR PRO PRO SER VAL TYR SEQRES 11 H 233 PRO LEU ALA PRO GLY CYS GLY ASP THR THR GLY SER SER SEQRES 12 H 233 VAL THR SER GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU SEQRES 13 H 233 PRO VAL THR VAL THR TRP ASN SER GLY SER LEU SER SER SEQRES 14 H 233 SER VAL HIS THR PHE PRO ALA LEU LEU GLN SER GLY LEU SEQRES 15 H 233 TYR THR MET SER SER SER VAL THR VAL PRO SER SER THR SEQRES 16 H 233 TRP PRO SER GLN THR VAL THR CYS SER VAL ALA HIS PRO SEQRES 17 H 233 ALA SER SER THR THR VAL ASP LYS LYS LEU GLU PRO SER SEQRES 18 H 233 GLY PRO ILE SER THR ILE ASN PRO CYS PRO PRO CYS HET ZN L 301 1 HET ACT L 302 4 HET ACT L 303 4 HET 2M9 H 501 30 HET PO4 H 502 5 HET ZN H 503 1 HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM 2M9 8-METHOXYPYRENE-1,3,6-TRISULFONIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 3 ZN 2(ZN 2+) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 6 2M9 C17 H12 O10 S3 FORMUL 7 PO4 O4 P 3- FORMUL 9 HOH *136(H2 O) HELIX 1 1 GLU L 79 VAL L 83 5 5 HELIX 2 2 SER L 121 SER L 127 1 7 HELIX 3 3 LYS L 183 HIS L 189 1 7 HELIX 4 4 THR H 28 TYR H 32 5 5 HELIX 5 5 GLN H 61 LYS H 64 5 4 HELIX 6 6 THR H 83 SER H 87 5 5 HELIX 7 7 SER H 163 SER H 165 5 3 HELIX 8 8 SER H 196 TRP H 199 5 3 HELIX 9 9 PRO H 213 SER H 216 5 4 SHEET 1 A 4 LEU L 4 SER L 7 0 SHEET 2 A 4 ALA L 19 ALA L 25 -1 O SER L 22 N SER L 7 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O LEU L 73 N ILE L 21 SHEET 4 A 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 B 6 SER L 10 SER L 14 0 SHEET 2 B 6 THR L 102 LYS L 107 1 O GLU L 105 N LEU L 11 SHEET 3 B 6 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 B 6 MET L 33 GLN L 38 -1 N HIS L 34 O GLN L 89 SHEET 5 B 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 B 6 ASN L 53 LEU L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 C 4 SER L 10 SER L 14 0 SHEET 2 C 4 THR L 102 LYS L 107 1 O GLU L 105 N LEU L 11 SHEET 3 C 4 ALA L 84 GLN L 90 -1 N ALA L 84 O LEU L 104 SHEET 4 C 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 D 2 ASP L 27C SER L 27D 0 SHEET 2 D 2 ASN L 30 SER L 31 -1 O ASN L 30 N SER L 27D SHEET 1 E 4 THR L 114 PHE L 118 0 SHEET 2 E 4 GLY L 129 PHE L 139 -1 O PHE L 135 N SER L 116 SHEET 3 E 4 TYR L 173 THR L 182 -1 O MET L 175 N LEU L 136 SHEET 4 E 4 VAL L 159 TRP L 163 -1 N LEU L 160 O THR L 178 SHEET 1 F 4 SER L 153 GLU L 154 0 SHEET 2 F 4 ASN L 145 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 F 4 SER L 191 THR L 197 -1 O THR L 197 N ASN L 145 SHEET 4 F 4 ILE L 205 ASN L 210 -1 O ILE L 205 N ALA L 196 SHEET 1 G 4 GLN H 3 GLN H 6 0 SHEET 2 G 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 G 4 THR H 77 LEU H 82 -1 O MET H 80 N MET H 20 SHEET 4 G 4 ALA H 67 ASP H 72 -1 N ASP H 72 O THR H 77 SHEET 1 H 6 GLU H 10 VAL H 12 0 SHEET 2 H 6 THR H 107 VAL H 111 1 O THR H 108 N GLU H 10 SHEET 3 H 6 ALA H 88 ARG H 95 -1 N TYR H 90 O THR H 107 SHEET 4 H 6 MET H 34 SER H 40 -1 N GLN H 39 O VAL H 89 SHEET 5 H 6 SER H 44 ILE H 51 -1 O GLU H 46 N LYS H 38 SHEET 6 H 6 ASN H 57 TYR H 59 -1 O GLY H 58 N TYR H 50 SHEET 1 I 4 GLU H 10 VAL H 12 0 SHEET 2 I 4 THR H 107 VAL H 111 1 O THR H 108 N GLU H 10 SHEET 3 I 4 ALA H 88 ARG H 95 -1 N TYR H 90 O THR H 107 SHEET 4 I 4 PHE H 100D TRP H 103 -1 O VAL H 102 N ARG H 94 SHEET 1 J 4 SER H 120 LEU H 124 0 SHEET 2 J 4 SER H 137 TYR H 147 -1 O LYS H 145 N SER H 120 SHEET 3 J 4 LEU H 184 PRO H 194 -1 O VAL H 193 N VAL H 138 SHEET 4 J 4 HIS H 172 GLN H 179 -1 N HIS H 172 O SER H 190 SHEET 1 K 3 THR H 153 TRP H 157 0 SHEET 2 K 3 THR H 206 HIS H 212 -1 O SER H 209 N THR H 156 SHEET 3 K 3 THR H 217 LYS H 222 -1 O THR H 217 N HIS H 212 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.19 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.10 SSBOND 3 CYS H 22 CYS H 92 1555 1555 2.12 SSBOND 4 CYS H 142 CYS H 208 1555 1555 2.07 LINK OE1 GLU L 27 ZN ZN L 301 1555 1555 1.97 LINK OE1 GLU L 93 ZN ZN L 301 1555 1555 2.03 LINK OD1 ASN L 138 ZN ZN H 503 1555 1555 2.39 LINK NE2 HIS H 172 ZN ZN H 503 1555 1555 2.13 CISPEP 1 SER L 7 PRO L 8 0 -6.34 CISPEP 2 ASN L 76 PRO L 77 0 0.22 CISPEP 3 ASP L 94 PRO L 95 0 -1.50 CISPEP 4 TYR L 140 PRO L 141 0 2.88 CISPEP 5 GLN L 156 ASN L 157 0 3.06 CISPEP 6 HIS H 41 GLY H 42 0 -21.09 CISPEP 7 ASN H 54 GLY H 55 0 -12.67 CISPEP 8 PRO H 126 GLY H 127 0 15.34 CISPEP 9 PHE H 148 PRO H 149 0 0.72 CISPEP 10 GLU H 150 PRO H 151 0 5.87 CISPEP 11 TRP H 199 PRO H 200 0 3.53 SITE 1 AC1 4 GLU L 27 GLU L 93 ASP L 151 HIS L 189 SITE 1 AC2 3 GLN L 37 PRO L 59 ASP L 82 SITE 1 AC3 1 LYS L 142 SITE 1 AC4 14 GLY H 97 TYR H 98 GLY H 99 ILE H 100 SITE 2 AC4 14 ARG H 100A GLY H 100B PRO H 200 SER H 202 SITE 3 AC4 14 PRO H 225 HOH H 601 TYR L 28 ASN L 30 SITE 4 AC4 14 PHE L 32 ARG L 50 SITE 1 AC5 4 TYR H 100C ASP H 101 ASP H 130 GLU L 55 SITE 1 AC6 3 HIS H 172 ASN L 138 HOH L 438 CRYST1 92.660 127.837 47.785 90.00 90.00 90.00 P 21 21 2 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 0.010792 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020927 0.00000