HEADER IMMUNE SYSTEM 17-AUG-15 5ACM TITLE MCG IMMUNOGLOBULIN VARIABLE DOMAIN WITH METHYLENE BLUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MCG; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: IG LAMBDA CHAIN V-II REGION MGC; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS IMMUNE SYSTEM, MCG, IMMUNOGLOBULIN VARIABLE DOMAIN, METHYLENE BLUE EXPDTA X-RAY DIFFRACTION AUTHOR B.BRUMSHTEIN,S.R.ESSWEIN,L.SALWINSKI,M.L.PHILLIPS,A.T.LY,D.CASCIO, AUTHOR 2 M.R.SAWAYA,D.S.EISENBERG REVDAT 5 20-NOV-24 5ACM 1 REMARK REVDAT 4 10-JAN-24 5ACM 1 REMARK REVDAT 3 13-SEP-17 5ACM 1 REMARK REVDAT 2 22-MAR-17 5ACM 1 JRNL REVDAT 1 02-DEC-15 5ACM 0 JRNL AUTH B.BRUMSHTEIN,S.R.ESSWEIN,L.SALWINSKI,M.L.PHILLIPS,A.T.LY, JRNL AUTH 2 D.CASCIO,M.R.SAWAYA,D.S.EISENBERG JRNL TITL INHIBITION BY SMALL-MOLECULE LIGANDS OF FORMATION OF AMYLOID JRNL TITL 2 FIBRILS OF AN IMMUNOGLOBULIN LIGHT CHAIN VARIABLE DOMAIN. JRNL REF ELIFE V. 4 10935 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26576950 JRNL DOI 10.7554/ELIFE.10935 REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 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) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 78400 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) : 0.111 REMARK 3 R VALUE (WORKING SET) : 0.110 REMARK 3 FREE R VALUE : 0.122 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4102 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) : 1.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5577 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.0710 REMARK 3 BIN FREE R VALUE SET COUNT : 315 REMARK 3 BIN FREE R VALUE : 0.0790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1596 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.54000 REMARK 3 B22 (A**2) : 5.44000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.58000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.004 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.004 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.006 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.230 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.986 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.983 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1698 ; 0.046 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1482 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2321 ; 3.272 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3432 ; 2.182 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 7.068 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;32.715 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 239 ;10.971 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;29.251 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 259 ; 0.244 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1952 ; 0.019 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 372 ; 0.015 ; 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): 875 ; 2.028 ; 1.440 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 874 ; 2.030 ; 1.440 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1090 ; 2.052 ; 2.167 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 823 ; 2.642 ; 1.734 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): 3180 ; 7.427 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 74 ;26.787 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3281 ; 8.157 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.907 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H,-K,L REMARK 3 TWIN FRACTION : 0.093 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 : 1.20 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 5ACM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1290063761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73808 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 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 4UNU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M REMARK 280 METHYLENE BLUE, PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 15.54000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 GLN A 1 REMARK 465 GLY B 0 REMARK 465 GLN B 1 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 LYS A 44 CE NZ REMARK 470 LYS A 47 CD CE NZ REMARK 470 SER B 2 OG 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 2028 O HOH B 2072 1.47 REMARK 500 O HOH B 2028 O HOH B 2073 1.69 REMARK 500 O HOH B 2030 O HOH B 2078 1.71 REMARK 500 O HOH A 2027 O HOH B 2050 1.81 REMARK 500 OG SER A 26 O HOH A 2029 1.89 REMARK 500 O HOH A 2021 O HOH A 2022 1.98 REMARK 500 O HOH A 2001 O HOH A 2052 1.99 REMARK 500 O HOH A 2017 O HOH A 2098 2.09 REMARK 500 O HOH A 2072 O HOH A 2075 2.19 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 PRO A 7 N PRO A 7 CA 0.103 REMARK 500 GLY A 15 CA GLY A 15 C -0.117 REMARK 500 GLN A 16 CD GLN A 16 NE2 -0.210 REMARK 500 SER A 17 CA SER A 17 CB -0.183 REMARK 500 SER A 17 C SER A 17 O 0.118 REMARK 500 VAL A 18 CB VAL A 18 CG2 -0.168 REMARK 500 TYR A 38 CG TYR A 38 CD2 -0.112 REMARK 500 PRO A 46 CA PRO A 46 CB -0.130 REMARK 500 PRO A 61 CA PRO A 61 CB 0.122 REMARK 500 ARG A 63 CB ARG A 63 CG -0.180 REMARK 500 ARG A 63 CG ARG A 63 CD 0.169 REMARK 500 SER A 69 C GLY A 70 N -0.189 REMARK 500 GLU A 85 CD GLU A 85 OE2 0.066 REMARK 500 TYR A 89 CD1 TYR A 89 CE1 0.103 REMARK 500 TYR A 89 CZ TYR A 89 CE2 -0.151 REMARK 500 TYR A 93 CE1 TYR A 93 CZ -0.119 REMARK 500 SER B 9 CB SER B 9 OG -0.089 REMARK 500 SER B 13 CB SER B 13 OG 0.092 REMARK 500 VAL B 18 CB VAL B 18 CG1 -0.184 REMARK 500 ILE B 20 CA ILE B 20 C 0.163 REMARK 500 SER B 27 CA SER B 27 CB 0.103 REMARK 500 TYR B 38 CD1 TYR B 38 CE1 -0.116 REMARK 500 TYR B 51 CZ TYR B 51 OH 0.109 REMARK 500 ARG B 56 CZ ARG B 56 NH1 -0.121 REMARK 500 ARG B 56 CZ ARG B 56 NH2 0.096 REMARK 500 SER B 58 CA SER B 58 CB 0.094 REMARK 500 GLY B 59 N GLY B 59 CA -0.146 REMARK 500 ARG B 63 CA ARG B 63 CB -0.174 REMARK 500 ARG B 63 CB ARG B 63 CG -0.209 REMARK 500 ARG B 63 CG ARG B 63 CD 0.292 REMARK 500 ARG B 63 CZ ARG B 63 NH2 -0.138 REMARK 500 GLU B 83 CD GLU B 83 OE1 -0.109 REMARK 500 TYR B 89 CE1 TYR B 89 CZ -0.103 REMARK 500 CYS B 90 CB CYS B 90 SG -0.125 REMARK 500 SER B 96 CB SER B 96 OG 0.099 REMARK 500 VAL B 109 CB VAL B 109 CG1 -0.143 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 TYR A 34 CB - CG - CD2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 56 NH1 - CZ - NH2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 PRO A 61 N - CA - CB ANGL. DEV. = -7.3 DEGREES REMARK 500 ASP A 62 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 63 CG - CD - NE ANGL. DEV. = -14.5 DEGREES REMARK 500 GLU A 85 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 TYR A 89 CD1 - CE1 - CZ ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 28 CB - CA - C ANGL. DEV. = 13.6 DEGREES REMARK 500 TYR B 38 CZ - CE2 - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 LYS B 47 CD - CE - NZ ANGL. DEV. = 15.9 DEGREES REMARK 500 ARG B 56 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP B 62 CB - CG - OD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG B 63 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 SER B 67 CA - CB - OG ANGL. DEV. = 16.7 DEGREES REMARK 500 TYR B 89 CB - CG - CD2 ANGL. DEV. = 3.7 DEGREES REMARK 500 TYR B 93 CZ - CE2 - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 GLU B 94 OE1 - CD - OE2 ANGL. DEV. = -12.7 DEGREES REMARK 500 ASP B 97 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 LYS B 106 CD - CE - NZ ANGL. DEV. = 19.2 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 ASP A 28 -96.62 -144.83 REMARK 500 TYR A 34 48.54 -143.73 REMARK 500 VAL A 53 -52.72 77.66 REMARK 500 ASN A 54 44.03 -154.23 REMARK 500 GLN B 16 -159.17 -87.42 REMARK 500 ASP B 28 -99.88 -138.92 REMARK 500 ASN B 33 67.08 -103.05 REMARK 500 TYR B 34 49.19 -142.58 REMARK 500 VAL B 53 -54.16 75.32 REMARK 500 ASN B 54 43.26 -152.49 REMARK 500 ALA B 86 170.70 178.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE B 99 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 59 10.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2095 DISTANCE = 5.87 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MBT A 1111 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1112 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1111 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1112 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1113 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ACL RELATED DB: PDB REMARK 900 MCG IMMUNOGLOBULIN VARIABLE DOMAIN WITH METHYLENE BLUE DBREF 5ACM A 1 110 UNP P01709 LV206_HUMAN 1 110 DBREF 5ACM B 1 110 UNP P01709 LV206_HUMAN 1 110 SEQADV 5ACM GLY A 0 UNP P01709 EXPRESSION TAG SEQADV 5ACM GLY B 0 UNP P01709 EXPRESSION TAG SEQRES 1 A 111 GLY GLN SER ALA LEU THR GLN PRO PRO SER ALA SER GLY SEQRES 2 A 111 SER LEU GLY GLN SER VAL THR ILE SER CYS THR GLY THR SEQRES 3 A 111 SER SER ASP VAL GLY GLY TYR ASN TYR VAL SER TRP TYR SEQRES 4 A 111 GLN GLN HIS ALA GLY LYS ALA PRO LYS VAL ILE ILE TYR SEQRES 5 A 111 GLU VAL ASN LYS ARG PRO SER GLY VAL PRO ASP ARG PHE SEQRES 6 A 111 SER GLY SER LYS SER GLY ASN THR ALA SER LEU THR VAL SEQRES 7 A 111 SER GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS SEQRES 8 A 111 SER SER TYR GLU GLY SER ASP ASN PHE VAL PHE GLY THR SEQRES 9 A 111 GLY THR LYS VAL THR VAL LEU SEQRES 1 B 111 GLY GLN SER ALA LEU THR GLN PRO PRO SER ALA SER GLY SEQRES 2 B 111 SER LEU GLY GLN SER VAL THR ILE SER CYS THR GLY THR SEQRES 3 B 111 SER SER ASP VAL GLY GLY TYR ASN TYR VAL SER TRP TYR SEQRES 4 B 111 GLN GLN HIS ALA GLY LYS ALA PRO LYS VAL ILE ILE TYR SEQRES 5 B 111 GLU VAL ASN LYS ARG PRO SER GLY VAL PRO ASP ARG PHE SEQRES 6 B 111 SER GLY SER LYS SER GLY ASN THR ALA SER LEU THR VAL SEQRES 7 B 111 SER GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS SEQRES 8 B 111 SER SER TYR GLU GLY SER ASP ASN PHE VAL PHE GLY THR SEQRES 9 B 111 GLY THR LYS VAL THR VAL LEU HET MBT A1111 20 HET SO4 A1112 5 HET SO4 A1113 5 HET SO4 A1114 5 HET SO4 A1115 5 HET SO4 B1111 5 HET SO4 B1112 5 HET GOL B1113 6 HETNAM MBT 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN MBT METHYLENE BLUE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MBT C16 H18 N3 S 1+ FORMUL 4 SO4 6(O4 S 2-) FORMUL 10 GOL C3 H8 O3 FORMUL 11 HOH *208(H2 O) HELIX 1 1 GLN A 81 GLU A 85 5 5 HELIX 2 2 GLN B 81 GLU B 85 5 5 SHEET 1 AA 4 SER A 9 GLY A 12 0 SHEET 2 AA 4 THR A 105 VAL A 109 1 O LYS A 106 N ALA A 10 SHEET 3 AA 4 ALA A 86 TYR A 93 -1 O ALA A 86 N VAL A 107 SHEET 4 AA 4 PHE A 99 PHE A 101 1 O VAL A 100 N SER A 92 SHEET 1 AB 5 SER A 9 GLY A 12 0 SHEET 2 AB 5 THR A 105 VAL A 109 1 O LYS A 106 N ALA A 10 SHEET 3 AB 5 ALA A 86 TYR A 93 -1 O ALA A 86 N VAL A 107 SHEET 4 AB 5 VAL A 35 GLN A 40 -1 O SER A 36 N SER A 91 SHEET 5 AB 5 LYS A 47 ILE A 50 -1 O LYS A 47 N GLN A 39 SHEET 1 AC 2 PHE A 99 PHE A 101 0 SHEET 2 AC 2 ALA A 86 TYR A 93 1 O SER A 92 N VAL A 100 SHEET 1 AD 3 VAL A 18 THR A 23 0 SHEET 2 AD 3 THR A 72 VAL A 77 -1 O ALA A 73 N CYS A 22 SHEET 3 AD 3 PHE A 64 SER A 69 -1 O SER A 65 N THR A 76 SHEET 1 BA 4 SER B 9 SER B 13 0 SHEET 2 BA 4 THR B 105 LEU B 110 1 O LYS B 106 N ALA B 10 SHEET 3 BA 4 ALA B 86 TYR B 93 -1 O ALA B 86 N VAL B 107 SHEET 4 BA 4 PHE B 99 PHE B 101 1 O VAL B 100 N SER B 92 SHEET 1 BB 5 SER B 9 SER B 13 0 SHEET 2 BB 5 THR B 105 LEU B 110 1 O LYS B 106 N ALA B 10 SHEET 3 BB 5 ALA B 86 TYR B 93 -1 O ALA B 86 N VAL B 107 SHEET 4 BB 5 VAL B 35 GLN B 40 -1 O SER B 36 N SER B 91 SHEET 5 BB 5 LYS B 47 ILE B 50 -1 O LYS B 47 N GLN B 39 SHEET 1 BC 2 PHE B 99 PHE B 101 0 SHEET 2 BC 2 ALA B 86 TYR B 93 1 O SER B 92 N VAL B 100 SHEET 1 BD 3 SER B 17 THR B 23 0 SHEET 2 BD 3 THR B 72 SER B 78 -1 O ALA B 73 N CYS B 22 SHEET 3 BD 3 PHE B 64 SER B 69 -1 O SER B 65 N THR B 76 SSBOND 1 CYS A 22 CYS A 90 1555 1555 2.03 SSBOND 2 CYS B 22 CYS B 90 1555 1555 2.08 SITE 1 AC1 8 TYR A 34 TYR A 93 ASP A 97 PHE A 99 SITE 2 AC1 8 SO4 A1113 TYR B 93 ASP B 97 PHE B 99 SITE 1 AC2 7 TYR A 34 SER A 36 TYR A 38 HOH A2045 SITE 2 AC2 7 HOH A2050 HOH A2110 HOH A2111 SITE 1 AC3 4 TYR B 32 ASN B 33 HOH B2044 HOH B2094 SITE 1 AC4 4 TYR A 32 ASN A 33 MBT A1111 HOH A2038 SITE 1 AC5 6 SER B 2 ALA B 3 TYR B 51 LYS B 55 SITE 2 AC5 6 THR B 103 HOH B2060 SITE 1 AC6 3 PRO A 61 ARG A 63 GLN A 81 SITE 1 AC7 7 ALA A 3 TYR A 51 LYS A 55 THR A 103 SITE 2 AC7 7 HOH A2004 HOH A2005 HOH A2063 SITE 1 AC8 3 SER B 17 VAL B 18 THR B 19 CRYST1 39.220 31.080 73.630 90.00 90.09 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025497 0.000000 0.000040 0.00000 SCALE2 0.000000 0.032175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013581 0.00000