HEADER HYDROLASE 11-FEB-15 4Y4V TITLE STRUCTURE OF HELICOBACTER PYLORI CSD6 IN THE D-ALA-BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL SECRETED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 13-330; COMPND 5 SYNONYM: CSD6; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THE CYS176 RESIDUE HAS BEEN OXIDIZED INTO THE SULFENIC COMPND 8 ACID (CSO) IN THE CHAIN A ONLY.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CONSERVED HYPOTHETICAL SECRETED PROTEIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 13-330; COMPND 13 SYNONYM: CSD6; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI 26695; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 GENE: C694_02665, HP_0518; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI 26695; SOURCE 11 ORGANISM_TAXID: 85962; SOURCE 12 STRAIN: 26695; SOURCE 13 GENE: C694_02665, HP_0518; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CSD6, CELL SHAPE, L, D-CARBOXYPEPTIDASE, HELICOBACTER PYLORI, HP0518, KEYWDS 2 FLAGELLIN, PEPTIDOGLYCAN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.S.KIM,H.N.IM,H.J.YOON,S.W.SUH REVDAT 6 06-NOV-24 4Y4V 1 REMARK REVDAT 5 23-MAR-22 4Y4V 1 REMARK REVDAT 4 18-OCT-17 4Y4V 1 JRNL REMARK REVDAT 3 21-OCT-15 4Y4V 1 JRNL REVDAT 2 09-SEP-15 4Y4V 1 JRNL REVDAT 1 02-SEP-15 4Y4V 0 JRNL AUTH H.S.KIM,H.N.IM,D.R.AN,J.Y.YOON,J.Y.JANG,S.MOBASHERY,D.HESEK, JRNL AUTH 2 M.LEE,J.YOO,M.CUI,S.CHOI,C.KIM,N.K.LEE,S.J.KIM,J.Y.KIM, JRNL AUTH 3 G.BANG,B.W.HAN,B.I.LEE,H.J.YOON,S.W.SUH JRNL TITL THE CELL SHAPE-DETERMINING CSD6 PROTEIN FROM HELICOBACTER JRNL TITL 2 PYLORI CONSTITUTES A NEW FAMILY OF L,D-CARBOXYPEPTIDASE JRNL REF J.BIOL.CHEM. V. 290 25103 2015 JRNL REFN ESSN 1083-351X JRNL PMID 26306031 JRNL DOI 10.1074/JBC.M115.658781 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 45096 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2400 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3224 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5249 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 315 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.19000 REMARK 3 B22 (A**2) : -1.66000 REMARK 3 B33 (A**2) : -0.53000 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): 0.198 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.124 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.612 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5407 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5155 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7252 ; 1.393 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11878 ; 0.903 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 628 ; 6.657 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;39.246 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1010 ;14.016 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.615 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 752 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6055 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1301 ; 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): 2533 ; 2.189 ; 3.523 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2533 ; 2.188 ; 3.523 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3154 ; 3.355 ; 5.266 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3155 ; 3.354 ; 5.266 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2874 ; 2.708 ; 3.887 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2874 ; 2.707 ; 3.887 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4099 ; 4.403 ; 5.670 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6272 ; 6.851 ;28.374 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6246 ; 6.809 ;28.330 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 4Y4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206624. 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 : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47575 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.780 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: ROD SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5%(V/V) TACSIMATE, 22%(W/V) PEG REMARK 280 3350, 100 MM SODIUM-HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 31.70200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.96000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.30350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.96000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.70200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.30350 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A -8 REMARK 465 GLY A -7 REMARK 465 SER A -6 REMARK 465 SER A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 LEU A 5 REMARK 465 VAL A 6 REMARK 465 PRO A 7 REMARK 465 ARG A 8 REMARK 465 GLY A 9 REMARK 465 SER A 10 REMARK 465 HIS A 11 REMARK 465 MET A 12 REMARK 465 VAL A 13 REMARK 465 GLY A 14 REMARK 465 MET B -8 REMARK 465 GLY B -7 REMARK 465 SER B -6 REMARK 465 SER B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 HIS B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 GLY B 4 REMARK 465 LEU B 5 REMARK 465 VAL B 6 REMARK 465 PRO B 7 REMARK 465 ARG B 8 REMARK 465 GLY B 9 REMARK 465 SER B 10 REMARK 465 HIS B 11 REMARK 465 MET B 12 REMARK 465 VAL B 13 REMARK 465 GLY B 14 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 CG ASN B 165 OD2 ASP B 167 1.98 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 PRO B 78 C - N - CD ANGL. DEV. = 15.7 DEGREES REMARK 500 PRO B 143 C - N - CD ANGL. DEV. = 15.0 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 130 137.23 -37.90 REMARK 500 ASN A 165 1.53 -68.30 REMARK 500 ASP A 203 -64.04 67.26 REMARK 500 ASN A 303 16.44 55.62 REMARK 500 GLU B 127 -40.53 -134.62 REMARK 500 ARG B 168 43.83 -145.42 REMARK 500 ASP B 203 -71.94 66.23 REMARK 500 ASN B 285 29.82 46.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DAL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DAL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DAL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 404 DBREF 4Y4V A 13 330 UNP O25255 O25255_HELPY 13 330 DBREF 4Y4V B 13 330 UNP O25255 O25255_HELPY 13 330 SEQADV 4Y4V MET A -8 UNP O25255 EXPRESSION TAG SEQADV 4Y4V GLY A -7 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER A -6 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER A -5 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS A -4 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS A -3 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS A -2 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS A -1 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS A 0 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS A 1 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER A 2 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER A 3 UNP O25255 EXPRESSION TAG SEQADV 4Y4V GLY A 4 UNP O25255 EXPRESSION TAG SEQADV 4Y4V LEU A 5 UNP O25255 EXPRESSION TAG SEQADV 4Y4V VAL A 6 UNP O25255 EXPRESSION TAG SEQADV 4Y4V PRO A 7 UNP O25255 EXPRESSION TAG SEQADV 4Y4V ARG A 8 UNP O25255 EXPRESSION TAG SEQADV 4Y4V GLY A 9 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER A 10 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS A 11 UNP O25255 EXPRESSION TAG SEQADV 4Y4V MET A 12 UNP O25255 EXPRESSION TAG SEQADV 4Y4V MET B -8 UNP O25255 EXPRESSION TAG SEQADV 4Y4V GLY B -7 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER B -6 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER B -5 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS B -4 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS B -3 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS B -2 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS B -1 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS B 0 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS B 1 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER B 2 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER B 3 UNP O25255 EXPRESSION TAG SEQADV 4Y4V GLY B 4 UNP O25255 EXPRESSION TAG SEQADV 4Y4V LEU B 5 UNP O25255 EXPRESSION TAG SEQADV 4Y4V VAL B 6 UNP O25255 EXPRESSION TAG SEQADV 4Y4V PRO B 7 UNP O25255 EXPRESSION TAG SEQADV 4Y4V ARG B 8 UNP O25255 EXPRESSION TAG SEQADV 4Y4V GLY B 9 UNP O25255 EXPRESSION TAG SEQADV 4Y4V SER B 10 UNP O25255 EXPRESSION TAG SEQADV 4Y4V HIS B 11 UNP O25255 EXPRESSION TAG SEQADV 4Y4V MET B 12 UNP O25255 EXPRESSION TAG SEQRES 1 A 339 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 339 LEU VAL PRO ARG GLY SER HIS MET VAL GLY LEU ASN ALA SEQRES 3 A 339 SER ASP ARG LEU LEU GLU ILE MET ARG LEU TYR GLN LYS SEQRES 4 A 339 GLN GLY LEU GLU MET VAL GLY GLN LYS LEU ASP SER TYR SEQRES 5 A 339 LEU ALA ASP LYS SER PHE TRP ALA GLU GLU LEU GLN ASN SEQRES 6 A 339 LYS ASP THR ASP PHE GLY TYR TYR GLN ASN LYS GLN PHE SEQRES 7 A 339 LEU PHE VAL ALA ASN LYS SER LYS PRO SER LEU GLU PHE SEQRES 8 A 339 TYR GLU ILE GLU ASN ASN MET LEU LYS LYS ILE ASN SER SEQRES 9 A 339 SER LYS ALA LEU VAL GLY SER LYS LYS GLY ASP LYS THR SEQRES 10 A 339 LEU GLU GLY ASP LEU ALA THR PRO ILE GLY VAL TYR ARG SEQRES 11 A 339 ILE THR GLN LYS LEU GLU ARG LEU ASP GLN TYR TYR GLY SEQRES 12 A 339 VAL LEU ALA PHE VAL THR ASN TYR PRO ASN LEU TYR ASP SEQRES 13 A 339 THR LEU LYS LYS ARG THR GLY HIS GLY ILE TRP VAL HIS SEQRES 14 A 339 GLY MET PRO LEU ASN GLY ASP ARG ASN GLU LEU ASN THR SEQRES 15 A 339 LYS GLY CSO ILE ALA ILE GLU ASN PRO LEU LEU SER SER SEQRES 16 A 339 TYR ASP LYS VAL LEU LYS GLY GLU LYS ALA PHE LEU ILE SEQRES 17 A 339 THR TYR GLU ASP LYS PHE PHE PRO SER THR LYS GLU GLU SEQRES 18 A 339 LEU SER MET ILE LEU SER SER LEU PHE GLN TRP LYS GLU SEQRES 19 A 339 ALA TRP ALA ARG GLY ASP PHE GLU ARG TYR MET ARG PHE SEQRES 20 A 339 TYR ASN PRO ASN PHE THR ARG TYR ASP GLY MET LYS PHE SEQRES 21 A 339 ASN ALA PHE LYS GLU TYR LYS LYS ARG VAL PHE ALA LYS SEQRES 22 A 339 ASN GLU LYS LYS ASN ILE ALA PHE SER SER ILE ASN VAL SEQRES 23 A 339 ILE PRO TYR PRO ASN SER GLN ASN LYS ARG LEU PHE TYR SEQRES 24 A 339 VAL VAL PHE ASP GLN ASP TYR LYS ALA TYR GLN HIS ASN SEQRES 25 A 339 LYS LEU SER TYR SER SER ASN SER GLN LYS GLU LEU TYR SEQRES 26 A 339 ILE GLU ILE GLU ASN ASN GLN VAL SER ILE ILE MET GLU SEQRES 27 A 339 LYS SEQRES 1 B 339 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 339 LEU VAL PRO ARG GLY SER HIS MET VAL GLY LEU ASN ALA SEQRES 3 B 339 SER ASP ARG LEU LEU GLU ILE MET ARG LEU TYR GLN LYS SEQRES 4 B 339 GLN GLY LEU GLU MET VAL GLY GLN LYS LEU ASP SER TYR SEQRES 5 B 339 LEU ALA ASP LYS SER PHE TRP ALA GLU GLU LEU GLN ASN SEQRES 6 B 339 LYS ASP THR ASP PHE GLY TYR TYR GLN ASN LYS GLN PHE SEQRES 7 B 339 LEU PHE VAL ALA ASN LYS SER LYS PRO SER LEU GLU PHE SEQRES 8 B 339 TYR GLU ILE GLU ASN ASN MET LEU LYS LYS ILE ASN SER SEQRES 9 B 339 SER LYS ALA LEU VAL GLY SER LYS LYS GLY ASP LYS THR SEQRES 10 B 339 LEU GLU GLY ASP LEU ALA THR PRO ILE GLY VAL TYR ARG SEQRES 11 B 339 ILE THR GLN LYS LEU GLU ARG LEU ASP GLN TYR TYR GLY SEQRES 12 B 339 VAL LEU ALA PHE VAL THR ASN TYR PRO ASN LEU TYR ASP SEQRES 13 B 339 THR LEU LYS LYS ARG THR GLY HIS GLY ILE TRP VAL HIS SEQRES 14 B 339 GLY MET PRO LEU ASN GLY ASP ARG ASN GLU LEU ASN THR SEQRES 15 B 339 LYS GLY CYS ILE ALA ILE GLU ASN PRO LEU LEU SER SER SEQRES 16 B 339 TYR ASP LYS VAL LEU LYS GLY GLU LYS ALA PHE LEU ILE SEQRES 17 B 339 THR TYR GLU ASP LYS PHE PHE PRO SER THR LYS GLU GLU SEQRES 18 B 339 LEU SER MET ILE LEU SER SER LEU PHE GLN TRP LYS GLU SEQRES 19 B 339 ALA TRP ALA ARG GLY ASP PHE GLU ARG TYR MET ARG PHE SEQRES 20 B 339 TYR ASN PRO ASN PHE THR ARG TYR ASP GLY MET LYS PHE SEQRES 21 B 339 ASN ALA PHE LYS GLU TYR LYS LYS ARG VAL PHE ALA LYS SEQRES 22 B 339 ASN GLU LYS LYS ASN ILE ALA PHE SER SER ILE ASN VAL SEQRES 23 B 339 ILE PRO TYR PRO ASN SER GLN ASN LYS ARG LEU PHE TYR SEQRES 24 B 339 VAL VAL PHE ASP GLN ASP TYR LYS ALA TYR GLN HIS ASN SEQRES 25 B 339 LYS LEU SER TYR SER SER ASN SER GLN LYS GLU LEU TYR SEQRES 26 B 339 ILE GLU ILE GLU ASN ASN GLN VAL SER ILE ILE MET GLU SEQRES 27 B 339 LYS MODRES 4Y4V CSO A 176 CYS MODIFIED RESIDUE HET CSO A 176 7 HET DAL A 401 6 HET DAL A 402 6 HET GOL A 403 6 HET GOL B 401 6 HET DAL B 402 6 HET GOL B 403 6 HET GOL B 404 6 HETNAM CSO S-HYDROXYCYSTEINE HETNAM DAL D-ALANINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSO C3 H7 N O3 S FORMUL 3 DAL 3(C3 H7 N O2) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 10 HOH *315(H2 O) HELIX 1 AA1 ASN A 16 GLY A 32 1 17 HELIX 2 AA2 GLY A 32 ALA A 45 1 14 HELIX 3 AA3 ASP A 46 GLN A 55 1 10 HELIX 4 AA4 ASP A 130 GLY A 134 5 5 HELIX 5 AA5 ASN A 144 LYS A 150 1 7 HELIX 6 AA6 GLU A 180 LYS A 192 1 13 HELIX 7 AA7 THR A 209 GLY A 230 1 22 HELIX 8 AA8 ASP A 231 PHE A 238 1 8 HELIX 9 AA9 LYS A 250 LYS A 264 1 15 HELIX 10 AB1 ASN B 16 GLY B 32 1 17 HELIX 11 AB2 GLY B 32 ALA B 45 1 14 HELIX 12 AB3 ASP B 46 GLN B 55 1 10 HELIX 13 AB4 ASP B 130 GLY B 134 5 5 HELIX 14 AB5 ASN B 144 LYS B 150 1 7 HELIX 15 AB6 GLU B 180 LYS B 192 1 13 HELIX 16 AB7 THR B 209 GLY B 230 1 22 HELIX 17 AB8 ASP B 231 PHE B 238 1 8 HELIX 18 AB9 LYS B 250 LYS B 264 1 15 SHEET 1 AA1 6 TYR A 63 TYR A 64 0 SHEET 2 AA1 6 LYS A 267 PRO A 279 -1 O VAL A 277 N TYR A 63 SHEET 3 AA1 6 ARG A 287 GLN A 301 -1 O ASP A 294 N SER A 273 SHEET 4 AA1 6 LYS A 304 GLU A 320 -1 O LEU A 315 N VAL A 291 SHEET 5 AA1 6 GLN A 323 GLU A 329 -1 O SER A 325 N GLU A 318 SHEET 6 AA1 6 TYR A 239 ARG A 245 1 N ASN A 240 O ILE A 326 SHEET 1 AA2 8 MET A 89 LYS A 97 0 SHEET 2 AA2 8 SER A 79 GLU A 86 -1 N PHE A 82 O ILE A 93 SHEET 3 AA2 8 GLN A 68 ASN A 74 -1 N LEU A 70 O TYR A 83 SHEET 4 AA2 8 ALA A 196 TYR A 201 1 O ILE A 199 N ALA A 73 SHEET 5 AA2 8 GLY A 118 LEU A 126 -1 N ILE A 122 O ALA A 196 SHEET 6 AA2 8 ALA A 137 THR A 140 -1 O ALA A 137 N LEU A 126 SHEET 7 AA2 8 TRP A 158 HIS A 160 -1 O VAL A 159 N PHE A 138 SHEET 8 AA2 8 ILE A 177 ALA A 178 1 O ILE A 177 N HIS A 160 SHEET 1 AA3 6 TYR B 63 TYR B 64 0 SHEET 2 AA3 6 LYS B 267 TYR B 280 -1 O VAL B 277 N TYR B 63 SHEET 3 AA3 6 ARG B 287 GLN B 301 -1 O TYR B 290 N ILE B 278 SHEET 4 AA3 6 LYS B 304 GLU B 320 -1 O SER B 311 N GLN B 295 SHEET 5 AA3 6 GLN B 323 GLU B 329 -1 O ILE B 327 N TYR B 316 SHEET 6 AA3 6 TYR B 239 ARG B 245 1 N ASN B 240 O ILE B 326 SHEET 1 AA4 8 MET B 89 LYS B 97 0 SHEET 2 AA4 8 SER B 79 GLU B 86 -1 N GLU B 84 O LYS B 91 SHEET 3 AA4 8 GLN B 68 ASN B 74 -1 N VAL B 72 O GLU B 81 SHEET 4 AA4 8 ALA B 196 TYR B 201 1 O PHE B 197 N PHE B 71 SHEET 5 AA4 8 GLY B 118 LEU B 126 -1 N GLY B 118 O THR B 200 SHEET 6 AA4 8 ALA B 137 THR B 140 -1 O ALA B 137 N LEU B 126 SHEET 7 AA4 8 TRP B 158 GLY B 161 -1 O VAL B 159 N PHE B 138 SHEET 8 AA4 8 ILE B 177 ILE B 179 1 O ILE B 177 N HIS B 160 LINK C GLY A 175 N CSO A 176 1555 1555 1.33 LINK C CSO A 176 N ILE A 177 1555 1555 1.34 LINK ND2 ASN B 165 OD2 ASP B 167 1555 1555 1.42 CISPEP 1 LYS A 77 PRO A 78 0 -13.10 CISPEP 2 TYR A 142 PRO A 143 0 -7.39 CISPEP 3 LYS B 77 PRO B 78 0 -11.65 CISPEP 4 TYR B 142 PRO B 143 0 -2.36 SITE 1 AC1 7 LYS A 107 GLU A 110 GLY A 111 GLY A 154 SITE 2 AC1 7 HIS A 155 HOH A 548 HOH A 550 SITE 1 AC2 7 TYR A 133 GLY A 156 TRP A 158 CSO A 176 SITE 2 AC2 7 HOH A 550 HOH A 642 HOH A 666 SITE 1 AC3 3 GLU A 81 TYR A 83 TYR A 201 SITE 1 AC4 3 ALA A 271 GLN B 29 LYS B 30 SITE 1 AC5 5 LYS B 107 GLU B 110 GLY B 111 GLY B 154 SITE 2 AC5 5 HIS B 155 SITE 1 AC6 7 TRP B 227 TYR B 257 LYS B 258 VAL B 261 SITE 2 AC6 7 LYS B 268 TYR B 297 HOH B 517 SITE 1 AC7 2 GLU B 81 TYR B 201 CRYST1 63.404 90.607 127.920 90.00 90.00 90.00 P 21 21 21 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 0.015772 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007817 0.00000