HEADER IMMUNE SYSTEM 22-JUN-21 7R63 TITLE NB82, A NANOBODY AGAINST VOLTAGE GATED SODIUM CHANNELS NAV1.4 AND TITLE 2 NAV1.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY NB82; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: NANOBODY VHH; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 GENE: VHH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA GAMMI 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHEN6 KEYWDS NANOBODY, VHH, NAV1.4, NAV1.5, VOLTAGE-GATED SODIUM CHANNEL, SCN4A, KEYWDS 2 SCN5A, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.SRINIVASAN,S.B.GABELLI REVDAT 3 30-OCT-24 7R63 1 REMARK REVDAT 2 18-OCT-23 7R63 1 REMARK REVDAT 1 04-MAY-22 7R63 0 JRNL AUTH L.SRINIVASAN,V.ALZOGARAY,D.SELVAKUMAR,S.NATHAN,J.B.YODER, JRNL AUTH 2 K.M.WRIGHT,S.KLINKE,J.N.NWAFOR,M.S.LABANDA,F.A.GOLDBAUM, JRNL AUTH 3 A.SCHON,E.FREIRE,G.F.TOMASELLI,L.M.AMZEL,M.BEN-JOHNY, JRNL AUTH 4 S.B.GABELLI JRNL TITL DEVELOPMENT OF HIGH-AFFINITY NANOBODIES SPECIFIC FOR NA V JRNL TITL 2 1.4 AND NA V 1.5 VOLTAGE-GATED SODIUM CHANNEL ISOFORMS. JRNL REF J.BIOL.CHEM. V. 298 01763 2022 JRNL REFN ESSN 1083-351X JRNL PMID 35202650 JRNL DOI 10.1016/J.JBC.2022.101763 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 35552 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1883 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2601 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 136 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3968 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 321 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.90000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -1.30000 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): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.042 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4111 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3672 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5565 ; 1.577 ; 1.652 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8499 ; 1.345 ; 1.579 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ; 8.127 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 227 ;31.370 ;21.145 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 647 ;16.129 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;18.724 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 506 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4649 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 927 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7R63 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37476 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.39400 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 REMARK 200 STARTING MODEL: 6H6J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-5% PEG MME 550, 0.1M BIS TRIS, 2.2M REMARK 280 AMMONIUM SULPHATE, PH 7.4, VAPOR DIFFUSION, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 85.35000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.35000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.87250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.23700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.87250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.23700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 85.35000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.87250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.23700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 85.35000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.87250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.23700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 360 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PHE A 129 REMARK 465 GLN A 130 REMARK 465 GLY A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 REMARK 465 ASN B 126 REMARK 465 LEU B 127 REMARK 465 TYR B 128 REMARK 465 PHE B 129 REMARK 465 GLN B 130 REMARK 465 GLY B 131 REMARK 465 HIS B 132 REMARK 465 HIS B 133 REMARK 465 HIS B 134 REMARK 465 HIS B 135 REMARK 465 HIS B 136 REMARK 465 HIS B 137 REMARK 465 GLY C 131 REMARK 465 HIS C 132 REMARK 465 HIS C 133 REMARK 465 HIS C 134 REMARK 465 HIS C 135 REMARK 465 HIS C 136 REMARK 465 HIS C 137 REMARK 465 GLY D 131 REMARK 465 HIS D 132 REMARK 465 HIS D 133 REMARK 465 HIS D 134 REMARK 465 HIS D 135 REMARK 465 HIS D 136 REMARK 465 HIS D 137 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 B 45 NE - CZ - NH2 ANGL. DEV. = -3.2 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 THR A 14 135.29 -39.23 REMARK 500 THR A 54 -167.46 -101.73 REMARK 500 LYS A 65 119.82 -31.41 REMARK 500 LEU A 127 31.92 -90.69 REMARK 500 ALA B 92 166.28 176.96 REMARK 500 THR C 14 131.98 -34.73 REMARK 500 THR C 54 -169.88 -106.28 REMARK 500 ALA C 92 164.50 179.46 REMARK 500 ALA D 92 163.22 176.51 REMARK 500 GLU D 125 -113.05 -132.41 REMARK 500 LEU D 127 -40.06 -154.84 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 A 384 DISTANCE = 6.36 ANGSTROMS 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 NA D 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 17 O REMARK 620 2 GLY D 8 O 20.1 REMARK 620 3 ARG D 19 O 23.0 3.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 35 O REMARK 620 2 SER B 37 OG 137.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 46 OE1 REMARK 620 2 PHE B 47 O 109.0 REMARK 620 3 SER B 61 OG 117.1 91.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA C 35 O REMARK 620 2 SER C 37 OG 144.1 REMARK 620 N 1 DBREF 7R63 A 1 137 PDB 7R63 7R63 1 137 DBREF 7R63 B 1 137 PDB 7R63 7R63 1 137 DBREF 7R63 C 1 137 PDB 7R63 7R63 1 137 DBREF 7R63 D 1 137 PDB 7R63 7R63 1 137 SEQRES 1 A 137 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 137 THR GLY GLY SER LEU ARG LEU SER CYS LYS ALA SER GLY SEQRES 3 A 137 ARG ALA PHE ALA ARG TYR ASP LEU ALA TRP SER ARG GLN SEQRES 4 A 137 ALA PRO GLY LYS GLN ARG GLU PHE VAL ALA SER ILE GLY SEQRES 5 A 137 VAL THR ARG ASN PRO PRO TYR TYR SER GLY SER VAL LYS SEQRES 6 A 137 GLY ARG PHE THR VAL SER ARG ASP ASN ALA LYS GLU THR SEQRES 7 A 137 VAL TYR LEU GLN MET ASN ASP LEU LYS PRO GLU ASP SER SEQRES 8 A 137 ALA VAL TYR TYR CYS ALA ALA LYS ASP ALA SER VAL THR SEQRES 9 A 137 VAL ALA THR ILE GLU ASP TYR PRO TYR TRP GLY ARG GLY SEQRES 10 A 137 THR GLN VAL THR VAL SER SER GLU ASN LEU TYR PHE GLN SEQRES 11 A 137 GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 137 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 137 THR GLY GLY SER LEU ARG LEU SER CYS LYS ALA SER GLY SEQRES 3 B 137 ARG ALA PHE ALA ARG TYR ASP LEU ALA TRP SER ARG GLN SEQRES 4 B 137 ALA PRO GLY LYS GLN ARG GLU PHE VAL ALA SER ILE GLY SEQRES 5 B 137 VAL THR ARG ASN PRO PRO TYR TYR SER GLY SER VAL LYS SEQRES 6 B 137 GLY ARG PHE THR VAL SER ARG ASP ASN ALA LYS GLU THR SEQRES 7 B 137 VAL TYR LEU GLN MET ASN ASP LEU LYS PRO GLU ASP SER SEQRES 8 B 137 ALA VAL TYR TYR CYS ALA ALA LYS ASP ALA SER VAL THR SEQRES 9 B 137 VAL ALA THR ILE GLU ASP TYR PRO TYR TRP GLY ARG GLY SEQRES 10 B 137 THR GLN VAL THR VAL SER SER GLU ASN LEU TYR PHE GLN SEQRES 11 B 137 GLY HIS HIS HIS HIS HIS HIS SEQRES 1 C 137 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 137 THR GLY GLY SER LEU ARG LEU SER CYS LYS ALA SER GLY SEQRES 3 C 137 ARG ALA PHE ALA ARG TYR ASP LEU ALA TRP SER ARG GLN SEQRES 4 C 137 ALA PRO GLY LYS GLN ARG GLU PHE VAL ALA SER ILE GLY SEQRES 5 C 137 VAL THR ARG ASN PRO PRO TYR TYR SER GLY SER VAL LYS SEQRES 6 C 137 GLY ARG PHE THR VAL SER ARG ASP ASN ALA LYS GLU THR SEQRES 7 C 137 VAL TYR LEU GLN MET ASN ASP LEU LYS PRO GLU ASP SER SEQRES 8 C 137 ALA VAL TYR TYR CYS ALA ALA LYS ASP ALA SER VAL THR SEQRES 9 C 137 VAL ALA THR ILE GLU ASP TYR PRO TYR TRP GLY ARG GLY SEQRES 10 C 137 THR GLN VAL THR VAL SER SER GLU ASN LEU TYR PHE GLN SEQRES 11 C 137 GLY HIS HIS HIS HIS HIS HIS SEQRES 1 D 137 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 137 THR GLY GLY SER LEU ARG LEU SER CYS LYS ALA SER GLY SEQRES 3 D 137 ARG ALA PHE ALA ARG TYR ASP LEU ALA TRP SER ARG GLN SEQRES 4 D 137 ALA PRO GLY LYS GLN ARG GLU PHE VAL ALA SER ILE GLY SEQRES 5 D 137 VAL THR ARG ASN PRO PRO TYR TYR SER GLY SER VAL LYS SEQRES 6 D 137 GLY ARG PHE THR VAL SER ARG ASP ASN ALA LYS GLU THR SEQRES 7 D 137 VAL TYR LEU GLN MET ASN ASP LEU LYS PRO GLU ASP SER SEQRES 8 D 137 ALA VAL TYR TYR CYS ALA ALA LYS ASP ALA SER VAL THR SEQRES 9 D 137 VAL ALA THR ILE GLU ASP TYR PRO TYR TRP GLY ARG GLY SEQRES 10 D 137 THR GLN VAL THR VAL SER SER GLU ASN LEU TYR PHE GLN SEQRES 11 D 137 GLY HIS HIS HIS HIS HIS HIS HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET PG0 A 204 8 HET NA B 201 1 HET NA B 202 1 HET SO4 B 203 5 HET SO4 B 204 5 HET PG0 B 205 8 HET NA C 201 1 HET SO4 C 202 5 HET CL C 203 1 HET NA D 201 1 HET SO4 D 202 5 HET SO4 D 203 5 HET PG0 D 204 8 HETNAM SO4 SULFATE ION HETNAM PG0 2-(2-METHOXYETHOXY)ETHANOL HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN PG0 PEG 6000 FORMUL 5 SO4 8(O4 S 2-) FORMUL 8 PG0 3(C5 H12 O3) FORMUL 9 NA 4(NA 1+) FORMUL 16 CL CL 1- FORMUL 21 HOH *321(H2 O) HELIX 1 AA1 ALA A 28 ALA A 30 5 3 HELIX 2 AA2 LYS A 87 SER A 91 5 5 HELIX 3 AA3 THR A 107 TYR A 111 5 5 HELIX 4 AA4 ALA B 28 ALA B 30 5 3 HELIX 5 AA5 LYS B 87 SER B 91 5 5 HELIX 6 AA6 THR B 107 TYR B 111 5 5 HELIX 7 AA7 ALA C 28 ALA C 30 5 3 HELIX 8 AA8 LYS C 87 SER C 91 5 5 HELIX 9 AA9 THR C 107 TYR C 111 5 5 HELIX 10 AB1 GLU C 125 PHE C 129 5 5 HELIX 11 AB2 ALA D 28 ALA D 30 5 3 HELIX 12 AB3 LYS D 87 SER D 91 5 5 HELIX 13 AB4 THR D 107 TYR D 111 5 5 SHEET 1 AA1 4 VAL A 2 SER A 7 0 SHEET 2 AA1 4 LEU A 18 GLY A 26 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 THR A 78 MET A 83 -1 O MET A 83 N LEU A 18 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N ASP A 73 O THR A 78 SHEET 1 AA212 GLY A 10 GLN A 13 0 SHEET 2 AA212 THR A 118 SER A 123 1 O THR A 121 N GLY A 10 SHEET 3 AA212 ALA A 92 ASP A 100 -1 N TYR A 94 O THR A 118 SHEET 4 AA212 TYR A 32 GLN A 39 -1 N SER A 37 O TYR A 95 SHEET 5 AA212 GLU A 46 ILE A 51 -1 O ALA A 49 N TRP A 36 SHEET 6 AA212 TYR A 59 SER A 61 -1 O SER A 61 N VAL A 48 SHEET 7 AA212 TYR D 59 SER D 61 -1 O TYR D 60 N TYR A 60 SHEET 8 AA212 GLU D 46 ILE D 51 -1 N VAL D 48 O SER D 61 SHEET 9 AA212 TYR D 32 GLN D 39 -1 N ARG D 38 O GLU D 46 SHEET 10 AA212 ALA D 92 ASP D 100 -1 O LYS D 99 N ASP D 33 SHEET 11 AA212 THR D 118 SER D 123 -1 O THR D 118 N TYR D 94 SHEET 12 AA212 GLY D 10 GLN D 13 1 N GLY D 10 O THR D 121 SHEET 1 AA310 TYR A 113 TRP A 114 0 SHEET 2 AA310 ALA A 92 ASP A 100 -1 N ALA A 98 O TYR A 113 SHEET 3 AA310 TYR A 32 GLN A 39 -1 N SER A 37 O TYR A 95 SHEET 4 AA310 GLU A 46 ILE A 51 -1 O ALA A 49 N TRP A 36 SHEET 5 AA310 TYR A 59 SER A 61 -1 O SER A 61 N VAL A 48 SHEET 6 AA310 TYR D 59 SER D 61 -1 O TYR D 60 N TYR A 60 SHEET 7 AA310 GLU D 46 ILE D 51 -1 N VAL D 48 O SER D 61 SHEET 8 AA310 TYR D 32 GLN D 39 -1 N ARG D 38 O GLU D 46 SHEET 9 AA310 ALA D 92 ASP D 100 -1 O LYS D 99 N ASP D 33 SHEET 10 AA310 TYR D 113 TRP D 114 -1 O TYR D 113 N ALA D 98 SHEET 1 AA4 4 VAL B 2 SER B 7 0 SHEET 2 AA4 4 LEU B 18 GLY B 26 -1 O SER B 21 N SER B 7 SHEET 3 AA4 4 THR B 78 MET B 83 -1 O MET B 83 N LEU B 18 SHEET 4 AA4 4 PHE B 68 ASP B 73 -1 N SER B 71 O TYR B 80 SHEET 1 AA5 6 GLY B 10 GLN B 13 0 SHEET 2 AA5 6 THR B 118 SER B 123 1 O THR B 121 N GLY B 10 SHEET 3 AA5 6 ALA B 92 ASP B 100 -1 N TYR B 94 O THR B 118 SHEET 4 AA5 6 TYR B 32 GLN B 39 -1 N SER B 37 O TYR B 95 SHEET 5 AA5 6 GLU B 46 ILE B 51 -1 O ALA B 49 N TRP B 36 SHEET 6 AA5 6 TYR B 59 TYR B 60 -1 O TYR B 59 N SER B 50 SHEET 1 AA6 4 GLY B 10 GLN B 13 0 SHEET 2 AA6 4 THR B 118 SER B 123 1 O THR B 121 N GLY B 10 SHEET 3 AA6 4 ALA B 92 ASP B 100 -1 N TYR B 94 O THR B 118 SHEET 4 AA6 4 TYR B 113 TRP B 114 -1 O TYR B 113 N ALA B 98 SHEET 1 AA7 4 VAL C 2 SER C 7 0 SHEET 2 AA7 4 LEU C 18 GLY C 26 -1 O SER C 25 N GLN C 3 SHEET 3 AA7 4 THR C 78 MET C 83 -1 O MET C 83 N LEU C 18 SHEET 4 AA7 4 PHE C 68 ASP C 73 -1 N THR C 69 O GLN C 82 SHEET 1 AA8 6 GLY C 10 GLN C 13 0 SHEET 2 AA8 6 THR C 118 SER C 123 1 O THR C 121 N GLY C 10 SHEET 3 AA8 6 ALA C 92 ASP C 100 -1 N TYR C 94 O THR C 118 SHEET 4 AA8 6 TYR C 32 GLN C 39 -1 N ASP C 33 O LYS C 99 SHEET 5 AA8 6 GLU C 46 ILE C 51 -1 O ALA C 49 N TRP C 36 SHEET 6 AA8 6 TYR C 59 TYR C 60 -1 O TYR C 59 N SER C 50 SHEET 1 AA9 4 GLY C 10 GLN C 13 0 SHEET 2 AA9 4 THR C 118 SER C 123 1 O THR C 121 N GLY C 10 SHEET 3 AA9 4 ALA C 92 ASP C 100 -1 N TYR C 94 O THR C 118 SHEET 4 AA9 4 TYR C 113 TRP C 114 -1 O TYR C 113 N ALA C 98 SHEET 1 AB1 4 GLN D 3 SER D 7 0 SHEET 2 AB1 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AB1 4 THR D 78 MET D 83 -1 O MET D 83 N LEU D 18 SHEET 4 AB1 4 PHE D 68 ASP D 73 -1 N SER D 71 O TYR D 80 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.04 SSBOND 2 CYS B 22 CYS B 96 1555 1555 2.08 SSBOND 3 CYS C 22 CYS C 96 1555 1555 2.04 SSBOND 4 CYS D 22 CYS D 96 1555 1555 2.06 LINK O SER B 17 NA NA D 201 1555 8555 2.72 LINK O ALA B 35 NA NA B 202 1555 1555 3.06 LINK OG SER B 37 NA NA B 202 1555 1555 2.55 LINK OE1 GLU B 46 NA NA B 201 1555 1555 2.80 LINK O PHE B 47 NA NA B 201 1555 1555 2.61 LINK OG SER B 61 NA NA B 201 1555 1555 2.59 LINK O ALA C 35 NA NA C 201 1555 1555 3.01 LINK OG SER C 37 NA NA C 201 1555 1555 2.72 LINK O GLY D 8 NA NA D 201 1555 1555 2.67 LINK O ARG D 19 NA NA D 201 1555 1555 3.14 CRYST1 77.745 82.474 170.700 90.00 90.00 90.00 C 2 2 21 32 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 0.012863 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005858 0.00000