HEADER HYDROLASE 07-MAY-20 7C25 TITLE GLYCOSIDASE WILD TYPE AT PH8.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOMALTOSE GLUCOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.205; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KRIBBELLA FLAVIDA (STRAIN DSM 17836 / JCM 10339 SOURCE 3 / NBRC 14399); SOURCE 4 ORGANISM_TAXID: 479435; SOURCE 5 STRAIN: DSM 17836 / JCM 10339 / NBRC 14399; SOURCE 6 GENE: KFLA_1896; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS GLYCOSIDE HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.TAGAMI,A.KIKUCHI,M.OKUYAMA,A.KIMURA REVDAT 3 29-NOV-23 7C25 1 REMARK REVDAT 2 23-FEB-22 7C25 1 JRNL REVDAT 1 12-MAY-21 7C25 0 JRNL AUTH T.TAGAMI,M.CHEN,Y.FURUNAGA,A.KIKUCHI,J.SADAHIRO,W.LANG, JRNL AUTH 2 M.OKUYAMA,Y.TANAKA,T.IWASAKI,M.YAO,A.KIMURA JRNL TITL STRUCTURAL INSIGHTS REVEAL THE SECOND BASE CATALYST OF JRNL TITL 2 ISOMALTOSE GLUCOHYDROLASE. JRNL REF FEBS J. V. 289 1118 2022 JRNL REFN ISSN 1742-464X JRNL PMID 34665923 JRNL DOI 10.1111/FEBS.16237 REMARK 2 REMARK 2 RESOLUTION. 1.51 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 74640 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.985 REMARK 3 FREE R VALUE TEST SET COUNT : 3721 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5534 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 293 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2864 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 415 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17100 REMARK 3 B22 (A**2) : -0.17100 REMARK 3 B33 (A**2) : 0.34100 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): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.069 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3061 ; 0.016 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2722 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4190 ; 1.947 ; 1.621 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6247 ; 1.744 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 387 ; 5.695 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;31.035 ;20.118 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 414 ;11.564 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.778 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 362 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3574 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 742 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 760 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 47 ; 0.240 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1538 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 289 ; 0.162 ; 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): 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): 1527 ; 2.717 ; 2.182 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1526 ; 2.704 ; 2.179 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1921 ; 2.897 ; 3.279 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1922 ; 2.897 ; 3.283 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1533 ; 3.680 ; 2.462 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1530 ; 3.680 ; 2.458 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2268 ; 4.086 ; 3.613 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2269 ; 4.085 ; 3.615 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): 5782 ; 4.212 ; 3.000 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7C25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300016684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74640 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 47.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 26.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 0.2650 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 24.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.32900 REMARK 200 FOR SHELL : 0.028 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: 5Z3A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE (PH8.0), 8% PEG REMARK 280 MONOMETHYL ETHER 2000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 52.73100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.73100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.73100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.73100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.73100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.73100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.73100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.73100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: MONOMERIC 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 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 568 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 688 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 760 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 777 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 THR A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 THR A 8 REMARK 465 ALA A 381 REMARK 465 ALA A 382 REMARK 465 LYS A 383 REMARK 465 ASP A 384 REMARK 465 ALA A 385 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 ARG A 17 CG CD NE CZ NH1 NH2 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 OE1 GLU A 374 N NH4 A 406 1.93 REMARK 500 OG SER A 226 O2 GOL A 402 2.07 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 GLY A 9 N GLY A 9 CA 0.128 REMARK 500 GLY A 9 CA GLY A 9 C 0.102 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 A 171 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 321 NE - CZ - NH2 ANGL. DEV. = -4.1 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 A 42 112.67 -161.60 REMARK 500 GLU A 102 71.51 -108.95 REMARK 500 THR A 112 -63.09 -94.29 REMARK 500 ASP A 127 14.34 -145.67 REMARK 500 VAL A 252 -76.28 -94.55 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 913 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 914 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A 915 DISTANCE = 6.43 ANGSTROMS DBREF 7C25 A 1 385 UNP D2PPM8 IMGH_KRIFD 1 385 SEQADV 7C25 MET A -19 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 GLY A -18 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 SER A -17 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 SER A -16 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 HIS A -15 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 HIS A -14 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 HIS A -13 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 HIS A -12 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 HIS A -11 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 HIS A -10 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 SER A -9 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 SER A -8 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 GLY A -7 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 LEU A -6 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 VAL A -5 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 PRO A -4 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 ARG A -3 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 GLY A -2 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 SER A -1 UNP D2PPM8 EXPRESSION TAG SEQADV 7C25 HIS A 0 UNP D2PPM8 EXPRESSION TAG SEQRES 1 A 405 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 405 LEU VAL PRO ARG GLY SER HIS MET THR THR SER ALA ARG SEQRES 3 A 405 ASP THR GLY LEU ASP SER HIS GLU LEU ALA ARG LEU HIS SEQRES 4 A 405 GLU LEU ALA ARG HIS SER HIS ALA VAL ILE THR ARG HIS SEQRES 5 A 405 GLN ASP ALA GLY GLY ALA TYR PRO ALA ALA PRO THR PHE SEQRES 6 A 405 SER ALA TYR ARG GLY TYR ALA TRP LEU ARG ASP GLY SER SEQRES 7 A 405 PHE THR ALA GLU GLY ILE SER ARG TYR GLY ASP VAL ALA SEQRES 8 A 405 SER ALA GLY ARG PHE HIS ASP TRP VAL ASP GLY VAL LEU SEQRES 9 A 405 ARG ARG ARG ARG GLY GLN VAL ASP ASP LEU LEU ALA ALA SEQRES 10 A 405 VAL ASP ARG GLY GLU VAL PRO SER ASN GLU GLY MET LEU SEQRES 11 A 405 PRO THR ARG PHE THR PHE ASP GLY ASN ASP GLY SER ASP SEQRES 12 A 405 PRO TRP TRP ASP PHE GLN THR ASP GLY TYR GLY MET TRP SEQRES 13 A 405 LEU TRP SER VAL VAL THR HIS ALA ALA ARG HIS GLY LEU SEQRES 14 A 405 ASP LEU GLU ARG TRP ARG ALA GLY ILE ASP VAL ALA VAL SEQRES 15 A 405 ASP TYR LEU LEU ALA PHE TRP ASP ARG PRO CYS TYR ASP SEQRES 16 A 405 TRP TRP GLU GLU HIS VAL GLU HIS ARG HIS VAL SER THR SEQRES 17 A 405 LEU GLY ALA ILE HIS GLY GLY LEU VAL ALA VAL GLY THR SEQRES 18 A 405 CSX ALA ALA LEU ARG SER ALA PRO TRP SER ALA ALA THR SEQRES 19 A 405 LEU GLN VAL ALA ALA ARG ILE ARG SER LEU VAL SER ALA SEQRES 20 A 405 GLU GLY VAL VAL ASP GLY HIS LEU VAL LYS TRP LEU GLY SEQRES 21 A 405 SER SER ALA VAL ASP GLY SER LEU PRO ALA CYS VAL VAL SEQRES 22 A 405 PRO PHE GLY LEU VAL PRO PRO ASP ASP ASP VAL ALA ALA SEQRES 23 A 405 MET THR ARG ALA ALA VAL ALA LYS ASP LEU ASP VAL ASP SEQRES 24 A 405 GLY GLY VAL HIS ARG PHE ALA ALA ASP VAL PHE TYR GLY SEQRES 25 A 405 GLY GLY GLN TRP ILE LEU LEU SER ALA LEU LEU GLY TRP SEQRES 26 A 405 ASN LEU ALA ALA ALA GLY ASP THR ALA GLY ALA LEU ARG SEQRES 27 A 405 HIS LEU ARG TRP ILE ALA ASP GLN ALA ASP ALA ASP GLY SEQRES 28 A 405 ASP LEU PRO GLU GLN VAL PRO HIS HIS LEU LEU HIS PRO SEQRES 29 A 405 GLY SER ARG ALA GLU TRP VAL ALA ARG TRP GLY THR VAL SEQRES 30 A 405 ALA THR PRO LEU LEU TRP SER HIS GLY MET TYR LEU ILE SEQRES 31 A 405 LEU ALA ASP GLU LEU GLY LEU LEU PRO PRO ALA ALA LYS SEQRES 32 A 405 ASP ALA MODRES 7C25 CSX A 202 CYS MODIFIED RESIDUE HET CSX A 202 14 HET GOL A 401 6 HET GOL A 402 6 HET GOL A 403 6 HET GOL A 404 6 HET CIT A 405 13 HET NH4 A 406 1 HETNAM CSX S-OXY CYSTEINE HETNAM GOL GLYCEROL HETNAM CIT CITRIC ACID HETNAM NH4 AMMONIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSX C3 H7 N O3 S FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 CIT C6 H8 O7 FORMUL 7 NH4 H4 N 1+ FORMUL 8 HOH *415(H2 O) HELIX 1 AA1 ASP A 11 GLN A 33 1 23 HELIX 2 AA2 TRP A 53 GLY A 68 1 16 HELIX 3 AA3 ASP A 69 ARG A 86 1 18 HELIX 4 AA4 ARG A 87 ARG A 100 1 14 HELIX 5 AA5 SER A 105 MET A 109 5 5 HELIX 6 AA6 ASP A 123 PHE A 128 1 6 HELIX 7 AA7 THR A 130 GLY A 148 1 19 HELIX 8 AA8 ASP A 150 ARG A 153 5 4 HELIX 9 AA9 TRP A 154 TRP A 169 1 16 HELIX 10 AB1 HIS A 185 THR A 201 1 17 HELIX 11 AB2 CSX A 202 ARG A 206 5 5 HELIX 12 AB3 TRP A 210 GLY A 229 1 20 HELIX 13 AB4 SER A 247 VAL A 252 5 6 HELIX 14 AB5 ASP A 262 LEU A 276 1 15 HELIX 15 AB6 VAL A 289 GLY A 293 5 5 HELIX 16 AB7 ILE A 297 ALA A 310 1 14 HELIX 17 AB8 ASP A 312 ASP A 325 1 14 HELIX 18 AB9 HIS A 343 GLY A 345 5 3 HELIX 19 AC1 SER A 346 GLY A 355 1 10 HELIX 20 AC2 LEU A 361 LEU A 375 1 15 SHEET 1 AA1 2 TYR A 51 ALA A 52 0 SHEET 2 AA1 2 PHE A 114 THR A 115 -1 O PHE A 114 N ALA A 52 SHEET 1 AA2 2 VAL A 230 VAL A 231 0 SHEET 2 AA2 2 HIS A 234 LEU A 235 -1 O HIS A 234 N VAL A 231 SHEET 1 AA3 2 ASP A 277 VAL A 278 0 SHEET 2 AA3 2 GLY A 281 VAL A 282 -1 O GLY A 281 N VAL A 278 SHEET 1 AA4 2 GLN A 295 TRP A 296 0 SHEET 2 AA4 2 GLN A 336 VAL A 337 -1 O VAL A 337 N GLN A 295 LINK C THR A 201 N ACSX A 202 1555 1555 1.32 LINK C THR A 201 N BCSX A 202 1555 1555 1.32 LINK C ACSX A 202 N ALA A 203 1555 1555 1.33 LINK C BCSX A 202 N ALA A 203 1555 1555 1.33 CISPEP 1 VAL A 253 PRO A 254 0 8.19 CISPEP 2 THR A 359 PRO A 360 0 -8.89 CRYST1 105.462 105.462 89.952 90.00 90.00 90.00 P 4 21 2 8 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 0.009482 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011117 0.00000