HEADER HYDROLASE 08-DEC-14 4X6K TITLE CRYSTAL STRUCTURE OF THE INTRAMOLECULAR TRANS-SIALIDASE FROM TITLE 2 RUMINOCOCCUS GNAVUS IN COMPLEX WITH SIASTATIN B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANHYDROSIALIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 243-723; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUMINOCOCCUS GNAVUS CC55_001C; SOURCE 3 ORGANISM_TAXID: 1073375; SOURCE 4 GENE: HMPREF1201_01421; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTRAMOLECULAR, TRANS-SIALIDASE, SIALIDASE, NEURAMINIDASE, SIASTATIN KEYWDS 2 B, INHIBITOR, COMPLEX, HYDROLASE, ANHYDROSIALIDASE EXPDTA X-RAY DIFFRACTION AUTHOR C.D.OWEN,L.E.TAILFORD,G.L.TAYLOR,N.JUGE REVDAT 3 10-JAN-24 4X6K 1 REMARK REVDAT 2 30-AUG-17 4X6K 1 REMARK SITE ATOM REVDAT 1 22-JUL-15 4X6K 0 JRNL AUTH L.E.TAILFORD,C.D.OWEN,J.WALSHAW,E.H.CROST,J.HARDY-GODDARD, JRNL AUTH 2 G.LE GALL,W.M.DE VOS,G.L.TAYLOR,N.JUGE JRNL TITL DISCOVERY OF INTRAMOLECULAR TRANS-SIALIDASES IN HUMAN GUT JRNL TITL 2 MICROBIOTA SUGGESTS NOVEL MECHANISMS OF MUCOSAL ADAPTATION. JRNL REF NAT COMMUN V. 6 7624 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 26154892 JRNL DOI 10.1038/NCOMMS8624 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : NULL 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1586 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2358 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3778 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 465 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.54000 REMARK 3 B22 (A**2) : 0.54000 REMARK 3 B33 (A**2) : -1.75000 REMARK 3 B12 (A**2) : 0.27000 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): 0.183 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.097 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3900 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3647 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5293 ; 1.898 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8291 ; 0.870 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 487 ; 7.491 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;37.068 ;25.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;13.524 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;12.547 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 568 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4491 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 878 ; 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): 1949 ; 2.234 ; 2.510 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1950 ; 2.234 ; 2.511 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2435 ; 2.879 ; 3.746 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 4X6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000205065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34757 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45800 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 2.5.6 REMARK 200 STARTING MODEL: 2SLI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MICROSEEDING INTO 1.2 M NAH2PO4, 0.8 M REMARK 280 K2HPO4, 0.1 M CAPS PH 10.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.55450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.61030 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.90267 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 49.55450 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 28.61030 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.90267 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 49.55450 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 28.61030 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.90267 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 57.22061 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 87.80533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 57.22061 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 87.80533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 57.22061 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 87.80533 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: 18100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 241 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 443 CG CD CE NZ 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 SER A 324 O HOH A 901 2.15 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 ASP A 274 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 274 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 322 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 322 NE - CZ - NH2 ANGL. DEV. = -5.0 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 239 -95.53 -98.91 REMARK 500 ILE A 258 66.23 74.27 REMARK 500 SER A 285 -158.30 -171.33 REMARK 500 ASP A 339 76.09 76.36 REMARK 500 ARG A 399 -150.85 -113.59 REMARK 500 SER A 491 36.01 -88.88 REMARK 500 SER A 528 -160.45 -172.53 REMARK 500 GLU A 531 -72.62 -99.02 REMARK 500 ASP A 669 -112.34 -147.88 REMARK 500 SER A 676 -112.40 -114.94 REMARK 500 LYS A 694 52.99 -90.79 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 A1359 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1360 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1361 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A1362 DISTANCE = 6.63 ANGSTROMS REMARK 525 HOH A1363 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A1364 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH A1365 DISTANCE = 7.74 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACE A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 3XR A 802 DBREF 4X6K A 243 723 UNP V8BWT1 V8BWT1_RUMGN 243 723 SEQADV 4X6K ALA A 238 UNP V8BWT1 EXPRESSION TAG SEQADV 4X6K ASP A 239 UNP V8BWT1 EXPRESSION TAG SEQADV 4X6K ILE A 240 UNP V8BWT1 EXPRESSION TAG SEQADV 4X6K GLY A 241 UNP V8BWT1 EXPRESSION TAG SEQADV 4X6K SER A 242 UNP V8BWT1 EXPRESSION TAG SEQRES 1 A 486 ALA ASP ILE GLY SER ASN ILE PHE TYR ALA GLY ASP ALA SEQRES 2 A 486 THR LYS SER ASN TYR PHE ARG ILE PRO SER LEU LEU ALA SEQRES 3 A 486 LEU ASP SER GLY THR VAL ILE ALA ALA ALA ASP ALA ARG SEQRES 4 A 486 TYR GLY GLY THR HIS ASP ALA LYS SER LYS ILE ASN THR SEQRES 5 A 486 ALA PHE ALA LYS SER THR ASP GLY GLY LYS THR TRP GLY SEQRES 6 A 486 GLN PRO THR LEU PRO LEU LYS PHE ASP ASP TYR VAL ALA SEQRES 7 A 486 LYS ASN ILE ASP TRP PRO ARG ASP SER VAL GLY LYS ASN SEQRES 8 A 486 VAL GLN ILE GLN GLY SER ALA SER TYR ILE ASP PRO VAL SEQRES 9 A 486 LEU LEU GLU ASP LYS GLU THR HIS ARG VAL PHE LEU PHE SEQRES 10 A 486 ALA ASP MET MET PRO ALA GLY ILE GLY SER SER ASN ALA SEQRES 11 A 486 SER VAL GLY SER GLY PHE LYS GLU VAL ASP GLY LYS LYS SEQRES 12 A 486 TYR LEU LYS LEU HIS TRP LYS ASP ASP ALA ALA GLY THR SEQRES 13 A 486 TYR ASP TYR SER VAL ARG GLU ASN GLY THR ILE TYR ASN SEQRES 14 A 486 ASP THR THR ASN SER ALA THR GLU TYR SER VAL ASP GLY SEQRES 15 A 486 GLU TYR ASN LEU TYR LYS ASN GLY ASN ALA MET LEU CYS SEQRES 16 A 486 LYS GLN TYR ASP TYR ASN PHE GLU GLY THR LYS LEU LEU SEQRES 17 A 486 GLU THR GLN THR ASP THR ASP VAL ASN MET ASN VAL PHE SEQRES 18 A 486 TYR LYS ASP ALA ASP PHE LYS VAL PHE PRO THR THR TYR SEQRES 19 A 486 LEU ALA MET LYS TYR SER ASP ASP GLU GLY GLU THR TRP SEQRES 20 A 486 SER ASP LEU GLN ILE VAL SER THR PHE LYS PRO GLU GLU SEQRES 21 A 486 SER LYS PHE LEU VAL LEU GLY PRO GLY VAL GLY LYS GLN SEQRES 22 A 486 ILE ALA ASN GLY GLU HIS ALA GLY ARG LEU ILE VAL PRO SEQRES 23 A 486 LEU TYR SER LYS SER SER ALA GLU LEU GLY PHE MET TYR SEQRES 24 A 486 SER ASP ASP HIS GLY ASN ASN TRP THR TYR VAL GLU ALA SEQRES 25 A 486 ASP GLN ASN THR GLY GLY ALA THR ALA GLU ALA GLN ILE SEQRES 26 A 486 VAL GLU MET PRO ASP GLY SER LEU LYS THR TYR LEU ARG SEQRES 27 A 486 THR GLY SER GLY TYR ILE ALA GLN VAL MET SER THR ASP SEQRES 28 A 486 GLY GLY GLU THR TRP SER GLU ARG VAL PRO LEU THR GLU SEQRES 29 A 486 ILE ALA THR THR GLY TYR GLY THR GLN LEU SER VAL ILE SEQRES 30 A 486 ASN TYR SER GLN PRO VAL ASP GLY LYS PRO ALA ILE LEU SEQRES 31 A 486 LEU SER ALA PRO ASN ALA THR ASN GLY ARG LYS ASN GLY SEQRES 32 A 486 LYS ILE TRP ILE GLY LEU ILE SER GLU THR GLY ASN SER SEQRES 33 A 486 GLY LYS ASP LYS TYR SER VAL ASP TRP LYS TYR CYS TYR SEQRES 34 A 486 SER VAL ASP THR PRO GLN MET GLY TYR SER TYR SER CYS SEQRES 35 A 486 LEU THR GLU LEU PRO ASP GLY GLU ILE GLY LEU LEU TYR SEQRES 36 A 486 GLU LYS TYR ASP SER TRP SER ARG ASN GLU LEU HIS LEU SEQRES 37 A 486 LYS ASN ILE LEU LYS TYR GLU ARG PHE ASN ILE ASP GLU SEQRES 38 A 486 LEU LYS VAL GLN PRO HET ACE A 801 3 HET 3XR A 802 15 HETNAM ACE ACETYL GROUP HETNAM 3XR (2S,3R,4S,5S)-2-(ACETYLAMINO)-5-CARBOXY-3,4- HETNAM 2 3XR DIHYDROXYPIPERIDINIUM FORMUL 2 ACE C2 H4 O FORMUL 3 3XR C8 H15 N2 O5 1+ FORMUL 4 HOH *465(H2 O) HELIX 1 AA1 VAL A 325 VAL A 329 5 5 HELIX 2 AA2 GLY A 363 ALA A 367 5 5 HELIX 3 AA3 SER A 491 LYS A 494 5 4 HELIX 4 AA4 SER A 653 ASP A 656 5 4 HELIX 5 AA5 ASN A 715 LYS A 720 1 6 SHEET 1 AA1 4 TYR A 255 ALA A 263 0 SHEET 2 AA1 4 VAL A 269 ARG A 276 -1 O ILE A 270 N LEU A 262 SHEET 3 AA1 4 ILE A 287 SER A 294 -1 O ASN A 288 N ALA A 275 SHEET 4 AA1 4 THR A 305 LEU A 308 -1 O THR A 305 N PHE A 291 SHEET 1 AA2 5 GLN A 488 ILE A 489 0 SHEET 2 AA2 5 TYR A 471 SER A 477 -1 N MET A 474 O GLN A 488 SHEET 3 AA2 5 ARG A 350 MET A 358 -1 N ALA A 355 O ALA A 473 SHEET 4 AA2 5 SER A 336 ASP A 345 -1 N SER A 336 O MET A 358 SHEET 5 AA2 5 GLY A 506 VAL A 507 1 O GLY A 506 N LEU A 342 SHEET 1 AA3 7 PHE A 373 VAL A 376 0 SHEET 2 AA3 7 LYS A 379 TRP A 386 -1 O TYR A 381 N LYS A 374 SHEET 3 AA3 7 TYR A 396 VAL A 398 -1 O TYR A 396 N LEU A 384 SHEET 4 AA3 7 THR A 403 ASN A 406 -1 O TYR A 405 N SER A 397 SHEET 5 AA3 7 SER A 411 VAL A 417 -1 O THR A 413 N ILE A 404 SHEET 6 AA3 7 LEU A 423 LYS A 425 -1 O TYR A 424 N SER A 416 SHEET 7 AA3 7 ASN A 428 ALA A 429 -1 O ASN A 428 N LYS A 425 SHEET 1 AA4 3 PHE A 373 VAL A 376 0 SHEET 2 AA4 3 LYS A 379 TRP A 386 -1 O TYR A 381 N LYS A 374 SHEET 3 AA4 3 PHE A 464 LYS A 465 -1 O LYS A 465 N HIS A 385 SHEET 1 AA5 2 LEU A 431 GLU A 440 0 SHEET 2 AA5 2 LYS A 443 ASN A 454 -1 O LEU A 445 N ASN A 438 SHEET 1 AA6 3 LEU A 501 LEU A 503 0 SHEET 2 AA6 3 LEU A 520 SER A 526 -1 O TYR A 525 N VAL A 502 SHEET 3 AA6 3 LYS A 509 GLN A 510 -1 N LYS A 509 O ILE A 521 SHEET 1 AA7 4 LEU A 501 LEU A 503 0 SHEET 2 AA7 4 LEU A 520 SER A 526 -1 O TYR A 525 N VAL A 502 SHEET 3 AA7 4 LEU A 532 SER A 537 -1 O GLY A 533 N LEU A 524 SHEET 4 AA7 4 THR A 545 GLU A 548 -1 O VAL A 547 N PHE A 534 SHEET 1 AA8 4 ALA A 560 GLU A 564 0 SHEET 2 AA8 4 LEU A 570 LEU A 574 -1 O LYS A 571 N VAL A 563 SHEET 3 AA8 4 ILE A 581 SER A 586 -1 O VAL A 584 N THR A 572 SHEET 4 AA8 4 VAL A 597 LEU A 599 -1 O LEU A 599 N ILE A 581 SHEET 1 AA9 4 SER A 612 VAL A 620 0 SHEET 2 AA9 4 LYS A 623 ALA A 630 -1 O SER A 629 N SER A 612 SHEET 3 AA9 4 LYS A 641 GLU A 649 -1 O TRP A 643 N LEU A 628 SHEET 4 AA9 4 TYR A 658 SER A 667 -1 O TYR A 666 N ILE A 642 SHEET 1 AB1 3 SER A 678 GLU A 682 0 SHEET 2 AB1 3 ILE A 688 GLU A 693 -1 O GLY A 689 N THR A 681 SHEET 3 AB1 3 LEU A 709 PHE A 714 -1 O LYS A 710 N TYR A 692 CISPEP 1 ASP A 239 ILE A 240 0 -5.95 CISPEP 2 ALA A 283 LYS A 284 0 3.02 SITE 1 AC1 4 VAL A 490 THR A 492 ASN A 543 TRP A 544 SITE 1 AC2 18 ARG A 257 ILE A 258 ARG A 276 ASP A 282 SITE 2 AC2 18 ILE A 338 ASP A 339 ASP A 356 SER A 364 SITE 3 AC2 18 ARG A 575 ARG A 637 TYR A 677 TRP A 698 SITE 4 AC2 18 HOH A 935 HOH A 981 HOH A1051 HOH A 992 SITE 5 AC2 18 HOH A 914 HOH A1180 CRYST1 99.109 99.109 131.708 90.00 90.00 120.00 H 3 9 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 0.010090 0.005825 0.000000 0.00000 SCALE2 0.000000 0.011651 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007593 0.00000