HEADER HYDROLASE 12-JUL-23 8K2J TITLE CRYSTAL STRUCTURE OF GROUP 3 OLIGOSACCHARIDE/MONOSACCHARIDE-RELEASING TITLE 2 BETA-N-ACETYLGALACTOSAMINIDASE NGADSSM, APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLIGOSACCHARIDE/MONOSACCHARIDE-RELEASING BETA-N- COMPND 3 ACETYLGALACTOSAMINIDASE; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METAGENOME; SOURCE 3 ORGANISM_TAXID: 256318; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSIDE HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SUMIDA,S.FUSHINOBU REVDAT 2 22-MAY-24 8K2J 1 JRNL REVDAT 1 24-APR-24 8K2J 0 JRNL AUTH T.SUMIDA,S.HIRAOKA,K.USUI,A.ISHIWATA,T.SENGOKU,K.A.STUBBS, JRNL AUTH 2 K.TANAKA,S.DEGUCHI,S.FUSHINOBU,T.NUNOURA JRNL TITL GENETIC AND FUNCTIONAL DIVERSITY OF JRNL TITL 2 BETA-N-ACETYLGALACTOSAMINE-TARGETING GLYCOSIDASES EXPANDED JRNL TITL 3 BY DEEP-SEA METAGENOME ANALYSIS. JRNL REF NAT COMMUN V. 15 3543 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38730244 JRNL DOI 10.1038/S41467-024-47653-2 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 59829 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3242 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3737 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.77 REMARK 3 BIN R VALUE (WORKING SET) : 1.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 212 REMARK 3 BIN FREE R VALUE : 1.0380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4302 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 401 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.74000 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): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.314 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4429 ; 0.015 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3998 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6024 ; 1.966 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9315 ; 0.696 ; 1.562 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 526 ; 6.854 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 42 ;11.119 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 734 ;15.118 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 646 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5068 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 908 ; 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): 2113 ; 2.567 ; 2.235 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2113 ; 2.565 ; 2.235 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2636 ; 3.396 ; 3.334 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2637 ; 3.396 ; 3.335 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2316 ; 4.362 ; 2.672 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2305 ; 4.294 ; 2.657 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3371 ; 6.100 ; 3.796 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4794 ; 7.294 ;29.081 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4716 ; 7.218 ;27.467 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 REMARK 4 REMARK 4 8K2J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300038886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64770 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 47.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M BIS-TRIS REMARK 280 PH 6.0, 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 213.67600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.68950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.68950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 320.51400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.68950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.68950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 106.83800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.68950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.68950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 320.51400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.68950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.68950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 106.83800 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 213.67600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 970 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1095 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 GLY A 24 REMARK 465 PRO A 25 REMARK 465 GLY A 26 REMARK 465 THR A 51 REMARK 465 THR A 52 REMARK 465 GLY A 53 REMARK 465 GLN A 54 REMARK 465 LYS A 256 REMARK 465 SER A 257 REMARK 465 SER A 258 REMARK 465 ARG A 259 REMARK 465 ARG A 564 REMARK 465 GLN A 565 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 72 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 123 CB - CA - C ANGL. DEV. = -13.7 DEGREES REMARK 500 ASP A 175 CB - CA - C ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG A 291 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 339 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 339 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 357 CG - CD - NE ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 364 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 364 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 412 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 505 NE - CZ - NH2 ANGL. DEV. = -4.7 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 GLU A 28 -57.34 111.97 REMARK 500 ASN A 92 90.88 -176.57 REMARK 500 ASP A 131 -68.80 -161.23 REMARK 500 GLU A 135 74.59 -117.83 REMARK 500 ALA A 215 59.06 -146.81 REMARK 500 ASP A 219 -3.43 69.06 REMARK 500 SER A 293 -101.36 -146.34 REMARK 500 LEU A 351 -61.43 -98.54 REMARK 500 ALA A 374 58.85 -145.24 REMARK 500 TRP A 420 -168.98 -111.38 REMARK 500 CYS A 424 -139.10 -156.69 REMARK 500 GLN A 428 -144.11 -103.34 REMARK 500 ASN A 464 44.29 -149.72 REMARK 500 ASP A 498 22.01 -145.42 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 ARG A 61 0.09 SIDE CHAIN REMARK 500 ARG A 116 0.09 SIDE CHAIN REMARK 500 ARG A 173 0.08 SIDE CHAIN REMARK 500 ARG A 302 0.11 SIDE CHAIN REMARK 500 ARG A 307 0.16 SIDE CHAIN REMARK 500 ARG A 357 0.13 SIDE CHAIN REMARK 500 ARG A 497 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8K2J A 24 565 PDB 8K2J 8K2J 24 565 SEQRES 1 A 542 GLY PRO GLY LYS GLU ASP ARG ILE LEU LYS VAL TRP THR SEQRES 2 A 542 VAL ASP PRO LEU VAL LYS VAL PHE ARG ASP SER GLU PRO SEQRES 3 A 542 VAL THR THR GLY GLN ALA LEU ALA GLU VAL ALA ARG GLY SEQRES 4 A 542 GLU ARG ALA THR LEU GLN ILE VAL ILE ARG CYS ALA LYS SEQRES 5 A 542 PRO ILE GLN GLU LEU HIS ALA LYS VAL GLY PRO LEU ALA SEQRES 6 A 542 LEU GLY SER ASN ALA LYS GLN VAL LEU GLU SER ALA PRO SEQRES 7 A 542 VAL ARG PHE VAL GLY TYR VAL PRO VAL ASP ARG PRO ILE SEQRES 8 A 542 PRO ARG PRO PRO LYS ASP GLN LEU ARG ARG PRO PRO ALA SEQRES 9 A 542 ASP PHE PRO ASP PRO LEU LEU GLU GLU LYS THR ILE ALA SEQRES 10 A 542 VAL ASP GLU ASN GLN VAL GLN PRO ILE TRP VAL THR VAL SEQRES 11 A 542 ALA VAL PRO THR ASN THR GLN PRO GLY LEU TYR GLN GLY SEQRES 12 A 542 SER VAL HIS ILE SER GLY ARG VAL ASP GLY ARG GLN ILE SEQRES 13 A 542 THR THR LYS VAL PRO VAL ALA ILE LYS VAL PHE ASP ILE SEQRES 14 A 542 GLU VAL GLY GLN SER ARG LEU TRP VAL THR ASN TRP PHE SEQRES 15 A 542 SER MET GLN SER ARG HIS MET LYS ILE ALA PRO GLU PRO SEQRES 16 A 542 ASP SER GLN GLN TYR TRP ALA LEU LEU SER ARG TYR ALA SEQRES 17 A 542 ARG ASN MET SER GLU HIS ARG GLN ASN VAL VAL LEU VAL SEQRES 18 A 542 SER PRO LEU SER LEU ALA THR PHE GLN LEU ASP LYS SER SEQRES 19 A 542 SER ARG MET GLU VAL ASP PHE SER ARG PHE ASP ARG TRP SEQRES 20 A 542 VAL ARG ILE PHE ILE ALA GLU GLY VAL ILE GLY ARG ILE SEQRES 21 A 542 GLU GLY GLY HIS LEU GLY GLY ARG SER SER ASP TRP GLU SEQRES 22 A 542 SER PRO PHE VAL VAL ARG ILE LYS GLU LEU ARG GLU GLY SEQRES 23 A 542 ASN ILE ILE THR LYS SER VAL ALA PRO THR SER GLU GLU SEQRES 24 A 542 ALA ASN GLN PHE TYR ALA GLN PHE LEU PRO ALA LEU VAL SEQRES 25 A 542 ASN HIS LEU ARG ASP ARG GLY TRP LEU GLU LYS TYR ALA SEQRES 26 A 542 GLN HIS LEU ALA ASP GLU PRO VAL ARG THR ASN ILE GLU SEQRES 27 A 542 SER TYR ARG ALA ILE SER LYS LEU VAL ARG LYS TYR ALA SEQRES 28 A 542 PRO GLU LEU LYS ILE ILE GLU ALA CYS HIS THR LYS ASP SEQRES 29 A 542 LEU ALA GLY ALA ILE ASP VAL TRP VAL PRO GLN LEU ASN SEQRES 30 A 542 PHE LEU HIS ASN ASP PHE GLU HIS TYR GLN LYS ARG GLN SEQRES 31 A 542 ARG ALA GLY ASP GLU VAL TRP PHE TYR THR CYS ILE TYR SEQRES 32 A 542 PRO GLN GLY GLU TYR ALA ASN ARG PHE ILE GLU GLN PRO SEQRES 33 A 542 LEU LEU LYS THR ARG LEU LEU HIS TRP ILE ASN TYR ARG SEQRES 34 A 542 TYR GLY MET THR GLY TYR LEU HIS TRP GLY TYR ASN GLN SEQRES 35 A 542 TRP GLY LYS ASP SER PRO PHE THR HIS THR THR LYS GLN SEQRES 36 A 542 HIS THR GLY GLN GLN TYR LEU PRO ALA GLY ASP PRO TRP SEQRES 37 A 542 ILE VAL TYR PRO GLY ARG ASP GLY PRO LEU ASP SER ILE SEQRES 38 A 542 ARG HIS GLU ALA MET CYS ASP GLY ILE ALA ASP TYR GLU SEQRES 39 A 542 LEU LEU SER MET LEU GLY GLU ARG ASP PRO GLU ALA ALA SEQRES 40 A 542 LYS ARG LEU VAL ASN ARG HIS VAL LEU ASP PHE ASP ARG SEQRES 41 A 542 TYR ASN CYS ASN VAL GLU ALA PHE ARG ALA THR ARG LEU SEQRES 42 A 542 GLU LEU LEU GLU LEU LEU SER ARG GLN HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *401(H2 O) HELIX 1 AA1 SER A 220 HIS A 237 1 18 HELIX 2 AA2 PHE A 264 GLU A 277 1 14 HELIX 3 AA3 SER A 320 ARG A 341 1 22 HELIX 4 AA4 TRP A 343 GLU A 345 5 3 HELIX 5 AA5 VAL A 356 THR A 358 5 3 HELIX 6 AA6 ASN A 359 ALA A 374 1 16 HELIX 7 AA7 GLN A 398 ASP A 405 1 8 HELIX 8 AA8 ASP A 405 ALA A 415 1 11 HELIX 9 AA9 LEU A 440 LEU A 445 1 6 HELIX 10 AB1 LEU A 445 GLY A 454 1 10 HELIX 11 AB2 SER A 503 ASP A 526 1 24 HELIX 12 AB3 ASP A 526 ARG A 536 1 11 HELIX 13 AB4 ASN A 547 SER A 563 1 17 SHEET 1 AA1 5 LEU A 32 VAL A 37 0 SHEET 2 AA1 5 ARG A 64 CYS A 73 -1 O VAL A 70 N TRP A 35 SHEET 3 AA1 5 GLN A 147 ALA A 154 -1 O ILE A 149 N ILE A 69 SHEET 4 AA1 5 ARG A 103 VAL A 110 -1 N ARG A 103 O TRP A 150 SHEET 5 AA1 5 ALA A 127 LEU A 134 -1 O PRO A 132 N GLY A 106 SHEET 1 AA2 5 LEU A 56 ARG A 61 0 SHEET 2 AA2 5 ARG A 177 GLU A 193 1 O PHE A 190 N VAL A 59 SHEET 3 AA2 5 GLY A 162 VAL A 174 -1 N ILE A 170 O THR A 181 SHEET 4 AA2 5 LEU A 87 LEU A 89 -1 N ALA A 88 O GLN A 165 SHEET 5 AA2 5 ASN A 92 LEU A 97 -1 O LEU A 97 N LEU A 87 SHEET 1 AA3 5 LEU A 56 ARG A 61 0 SHEET 2 AA3 5 ARG A 177 GLU A 193 1 O PHE A 190 N VAL A 59 SHEET 3 AA3 5 GLY A 162 VAL A 174 -1 N ILE A 170 O THR A 181 SHEET 4 AA3 5 ILE A 77 VAL A 84 -1 N LYS A 83 O HIS A 169 SHEET 5 AA3 5 ILE A 139 VAL A 141 -1 O VAL A 141 N ILE A 77 SHEET 1 AA4 3 TRP A 200 ASN A 203 0 SHEET 2 AA4 3 GLY A 457 HIS A 460 1 O TYR A 458 N TRP A 200 SHEET 3 AA4 3 PHE A 421 TYR A 422 1 N PHE A 421 O LEU A 459 SHEET 1 AA5 6 VAL A 241 VAL A 244 0 SHEET 2 AA5 6 ARG A 282 GLY A 285 1 O GLU A 284 N VAL A 242 SHEET 3 AA5 6 TYR A 347 HIS A 350 1 O ALA A 348 N GLY A 285 SHEET 4 AA5 6 ILE A 379 CYS A 383 1 O ILE A 380 N GLN A 349 SHEET 5 AA5 6 VAL A 394 PRO A 397 1 O VAL A 396 N GLU A 381 SHEET 6 AA5 6 GLU A 418 VAL A 419 1 O GLU A 418 N TRP A 395 SHEET 1 AA6 2 THR A 251 GLN A 253 0 SHEET 2 AA6 2 GLU A 261 ASP A 263 -1 O ASP A 263 N THR A 251 SHEET 1 AA7 3 GLY A 289 ARG A 291 0 SHEET 2 AA7 3 PHE A 299 ARG A 307 -1 O VAL A 300 N GLY A 290 SHEET 3 AA7 3 ASN A 310 VAL A 316 -1 O ASN A 310 N ARG A 307 SHEET 1 AA8 2 VAL A 493 PRO A 495 0 SHEET 2 AA8 2 PRO A 500 ASP A 502 -1 O LEU A 501 N TYR A 494 SHEET 1 AA9 2 VAL A 538 ASP A 540 0 SHEET 2 AA9 2 ARG A 543 TYR A 544 -1 O ARG A 543 N LEU A 539 CISPEP 1 PRO A 125 PRO A 126 0 -4.14 CISPEP 2 ILE A 280 GLY A 281 0 -2.32 CISPEP 3 TYR A 426 PRO A 427 0 -1.10 CRYST1 53.379 53.379 427.352 90.00 90.00 90.00 P 43 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 0.018734 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002340 0.00000