HEADER HYDROLASE 02-FEB-06 2DDT TITLE CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUS WITH TITLE 2 MAGNESIUM ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOMYELIN PHOSPHODIESTERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SPHINGOMYELINASE; COMPND 5 EC: 3.1.4.12; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 STRAIN: IAM 1029; SOURCE 5 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1423; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ISW1214; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHY300PLK KEYWDS DNASE I LIKE FOLDING, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, RSGI, STRUCTURAL GENOMICS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.AGO,M.ODA,H.TSUGE,N.KATUNUMA,M.MIYANO,J.SAKURAI,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 13-MAR-24 2DDT 1 REMARK LINK REVDAT 3 24-FEB-09 2DDT 1 VERSN REVDAT 2 04-JUL-06 2DDT 1 JRNL REVDAT 1 02-MAY-06 2DDT 0 JRNL AUTH H.AGO,M.ODA,M.TAKAHASHI,H.TSUGE,S.OCHI,N.KATUNUMA,M.MIYANO, JRNL AUTH 2 J.SAKURAI JRNL TITL STRUCTURAL BASIS OF THE SPHINGOMYELIN PHOSPHODIESTERASE JRNL TITL 2 ACTIVITY IN NEUTRAL SPHINGOMYELINASE FROM BACILLUS CEREUS. JRNL REF J.BIOL.CHEM. V. 281 16157 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16595670 JRNL DOI 10.1074/JBC.M601089200 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 48541 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2438 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3483 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4570 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 534 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : -0.32000 REMARK 3 B12 (A**2) : 0.40000 REMARK 3 B13 (A**2) : 0.76000 REMARK 3 B23 (A**2) : 0.66000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.164 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.971 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4722 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3998 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6411 ; 2.161 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9398 ; 3.637 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 569 ; 2.014 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 227 ;39.418 ;25.771 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 771 ;10.911 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;16.469 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 697 ; 0.268 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5223 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 891 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1000 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4020 ; 0.246 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2316 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2085 ; 0.112 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 291 ; 0.122 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.104 ; 0.200 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): 20 ; 0.293 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 49 ; 0.263 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.167 ; 0.200 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): 3717 ; 1.820 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1156 ; 0.392 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4654 ; 2.062 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2243 ; 3.221 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1757 ; 3.998 ; 4.500 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 2DDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48543 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 90.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 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 <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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% (W/V) PEG 8000, 0.2M MAGNESIUM REMARK 280 SULFATE, 0.1MM CALCIUM CHROLIDE, 0.1M MES, PH 6.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 GLU A 1 REMARK 465 VAL A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 GLN A 6 REMARK 465 ASN A 7 REMARK 465 GLY A 124 REMARK 465 PRO A 125 REMARK 465 ASP A 126 REMARK 465 ASP A 156 REMARK 465 SER A 157 REMARK 465 MET A 158 REMARK 465 CYS A 159 REMARK 465 GLY A 160 REMARK 465 LYS A 161 REMARK 465 THR A 162 REMARK 465 LYS A 306 REMARK 465 GLU B 1 REMARK 465 VAL B 2 REMARK 465 SER B 3 REMARK 465 THR B 4 REMARK 465 THR B 5 REMARK 465 GLN B 6 REMARK 465 ASN B 7 REMARK 465 GLY B 124 REMARK 465 PRO B 125 REMARK 465 ASP B 126 REMARK 465 ASN B 127 REMARK 465 ASP B 156 REMARK 465 SER B 157 REMARK 465 MET B 158 REMARK 465 CYS B 159 REMARK 465 GLY B 160 REMARK 465 LYS B 161 REMARK 465 THR B 162 REMARK 465 LYS B 306 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 ASN B 141 N ASP B 142 1.76 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 LYS A 139 C LYS A 140 N -0.237 REMARK 500 LYS B 139 C LYS B 140 N -0.227 REMARK 500 ASN B 141 C ASP B 142 N -0.287 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 ASN B 141 CA - C - N ANGL. DEV. = 24.1 DEGREES REMARK 500 ASN B 141 O - C - N ANGL. DEV. = -26.3 DEGREES REMARK 500 ASP B 142 C - N - CA ANGL. DEV. = 15.9 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 MET A 19 67.84 -109.25 REMARK 500 SER A 82 35.03 -145.16 REMARK 500 ASN A 92 48.23 -75.38 REMARK 500 HIS A 261 -158.64 -134.88 REMARK 500 MET B 19 69.16 -110.54 REMARK 500 SER B 82 34.45 -143.74 REMARK 500 ASN B 92 48.71 -75.92 REMARK 500 ASN B 141 73.58 42.44 REMARK 500 ASN B 202 30.99 78.20 REMARK 500 ASN B 205 52.11 -113.40 REMARK 500 ASN B 207 2.82 -57.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN B 141 -15.54 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 310 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 53 OE1 REMARK 620 2 HOH A 322 O 89.4 REMARK 620 3 HOH A 326 O 91.8 97.5 REMARK 620 4 HOH A 352 O 175.3 89.9 83.7 REMARK 620 5 HOH A 367 O 90.5 96.4 165.9 94.2 REMARK 620 6 HOH A 384 O 91.1 178.8 81.3 89.5 84.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 311 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 55 O REMARK 620 2 ASN A 57 OD1 85.7 REMARK 620 3 GLU A 99 OE1 100.8 172.0 REMARK 620 4 ASP A 100 OD2 96.1 89.5 94.4 REMARK 620 5 HOH A 330 O 163.9 83.9 88.8 96.1 REMARK 620 6 HOH A 372 O 84.2 92.7 83.4 177.8 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 308 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 53 OE1 REMARK 620 2 HOH B 328 O 84.7 REMARK 620 3 HOH B 334 O 92.8 93.1 REMARK 620 4 HOH B 351 O 89.9 96.2 170.6 REMARK 620 5 HOH B 353 O 170.7 88.9 94.2 84.2 REMARK 620 6 HOH B 386 O 97.6 176.4 89.6 81.1 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 309 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 55 O REMARK 620 2 ASN B 57 OD1 84.2 REMARK 620 3 GLU B 99 OE1 103.5 171.2 REMARK 620 4 ASP B 100 OD2 94.3 89.1 94.7 REMARK 620 5 HOH B 383 O 86.6 93.9 82.3 176.9 REMARK 620 6 HOH B 400 O 166.6 83.4 88.5 90.5 89.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DDR RELATED DB: PDB REMARK 900 RELATED ID: 2DDS RELATED DB: PDB REMARK 900 RELATED ID: AR_001000745.3 RELATED DB: TARGETDB DBREF 2DDT A 1 306 UNP P11889 PHL2_BACCE 28 333 DBREF 2DDT B 1 306 UNP P11889 PHL2_BACCE 28 333 SEQRES 1 A 306 GLU VAL SER THR THR GLN ASN ASP THR LEU LYS VAL MET SEQRES 2 A 306 THR HIS ASN VAL TYR MET LEU SER THR ASN LEU TYR PRO SEQRES 3 A 306 ASN TRP GLY GLN THR GLU ARG ALA ASP LEU ILE GLY ALA SEQRES 4 A 306 ALA ASP TYR ILE LYS ASN GLN ASP VAL VAL ILE LEU ASN SEQRES 5 A 306 GLU VAL PHE ASP ASN SER ALA SER ASP ARG LEU LEU GLY SEQRES 6 A 306 ASN LEU LYS LYS GLU TYR PRO ASN GLN THR ALA VAL LEU SEQRES 7 A 306 GLY ARG SER SER GLY SER GLU TRP ASP LYS THR LEU GLY SEQRES 8 A 306 ASN TYR SER SER SER THR PRO GLU ASP GLY GLY VAL ALA SEQRES 9 A 306 ILE VAL SER LYS TRP PRO ILE ALA GLU LYS ILE GLN TYR SEQRES 10 A 306 VAL PHE ALA LYS GLY CYS GLY PRO ASP ASN LEU SER ASN SEQRES 11 A 306 LYS GLY PHE VAL TYR THR LYS ILE LYS LYS ASN ASP ARG SEQRES 12 A 306 PHE VAL HIS VAL ILE GLY THR HIS LEU GLN ALA GLU ASP SEQRES 13 A 306 SER MET CYS GLY LYS THR SER PRO ALA SER VAL ARG THR SEQRES 14 A 306 ASN GLN LEU LYS GLU ILE GLN ASP PHE ILE LYS ASN LYS SEQRES 15 A 306 ASN ILE PRO ASN ASN GLU TYR VAL LEU ILE GLY GLY ASP SEQRES 16 A 306 MET ASN VAL ASN LYS ILE ASN ALA GLU ASN ASN ASN ASP SEQRES 17 A 306 SER GLU TYR ALA SER MET PHE LYS THR LEU ASN ALA SER SEQRES 18 A 306 VAL PRO SER TYR THR GLY HIS THR ALA THR TRP ASP ALA SEQRES 19 A 306 THR THR ASN SER ILE ALA LYS TYR ASN PHE PRO ASP SER SEQRES 20 A 306 PRO ALA GLU TYR LEU ASP TYR ILE ILE ALA SER LYS ASP SEQRES 21 A 306 HIS ALA ASN PRO SER TYR ILE GLU ASN LYS VAL LEU GLN SEQRES 22 A 306 PRO LYS SER PRO GLN TRP THR VAL THR SER TRP PHE GLN SEQRES 23 A 306 LYS TYR THR TYR ASN ASP TYR SER ASP HIS TYR PRO VAL SEQRES 24 A 306 GLU ALA THR ILE SER MET LYS SEQRES 1 B 306 GLU VAL SER THR THR GLN ASN ASP THR LEU LYS VAL MET SEQRES 2 B 306 THR HIS ASN VAL TYR MET LEU SER THR ASN LEU TYR PRO SEQRES 3 B 306 ASN TRP GLY GLN THR GLU ARG ALA ASP LEU ILE GLY ALA SEQRES 4 B 306 ALA ASP TYR ILE LYS ASN GLN ASP VAL VAL ILE LEU ASN SEQRES 5 B 306 GLU VAL PHE ASP ASN SER ALA SER ASP ARG LEU LEU GLY SEQRES 6 B 306 ASN LEU LYS LYS GLU TYR PRO ASN GLN THR ALA VAL LEU SEQRES 7 B 306 GLY ARG SER SER GLY SER GLU TRP ASP LYS THR LEU GLY SEQRES 8 B 306 ASN TYR SER SER SER THR PRO GLU ASP GLY GLY VAL ALA SEQRES 9 B 306 ILE VAL SER LYS TRP PRO ILE ALA GLU LYS ILE GLN TYR SEQRES 10 B 306 VAL PHE ALA LYS GLY CYS GLY PRO ASP ASN LEU SER ASN SEQRES 11 B 306 LYS GLY PHE VAL TYR THR LYS ILE LYS LYS ASN ASP ARG SEQRES 12 B 306 PHE VAL HIS VAL ILE GLY THR HIS LEU GLN ALA GLU ASP SEQRES 13 B 306 SER MET CYS GLY LYS THR SER PRO ALA SER VAL ARG THR SEQRES 14 B 306 ASN GLN LEU LYS GLU ILE GLN ASP PHE ILE LYS ASN LYS SEQRES 15 B 306 ASN ILE PRO ASN ASN GLU TYR VAL LEU ILE GLY GLY ASP SEQRES 16 B 306 MET ASN VAL ASN LYS ILE ASN ALA GLU ASN ASN ASN ASP SEQRES 17 B 306 SER GLU TYR ALA SER MET PHE LYS THR LEU ASN ALA SER SEQRES 18 B 306 VAL PRO SER TYR THR GLY HIS THR ALA THR TRP ASP ALA SEQRES 19 B 306 THR THR ASN SER ILE ALA LYS TYR ASN PHE PRO ASP SER SEQRES 20 B 306 PRO ALA GLU TYR LEU ASP TYR ILE ILE ALA SER LYS ASP SEQRES 21 B 306 HIS ALA ASN PRO SER TYR ILE GLU ASN LYS VAL LEU GLN SEQRES 22 B 306 PRO LYS SER PRO GLN TRP THR VAL THR SER TRP PHE GLN SEQRES 23 B 306 LYS TYR THR TYR ASN ASP TYR SER ASP HIS TYR PRO VAL SEQRES 24 B 306 GLU ALA THR ILE SER MET LYS HET MG A 310 1 HET MG A 311 1 HET SO4 A 312 5 HET MES A 313 12 HET MG B 308 1 HET MG B 309 1 HET SO4 B 313 5 HET MES B 307 12 HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 3 MG 4(MG 2+) FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 MES 2(C6 H13 N O4 S) FORMUL 11 HOH *534(H2 O) HELIX 1 1 GLY A 29 ALA A 40 1 12 HELIX 2 2 ASP A 56 LYS A 68 1 13 HELIX 3 3 SER A 163 ASN A 183 1 21 HELIX 4 4 SER A 209 ASN A 219 1 11 HELIX 5 5 ASN A 237 PHE A 244 1 8 HELIX 6 6 GLY B 29 ALA B 40 1 12 HELIX 7 7 ASP B 56 LYS B 68 1 13 HELIX 8 8 SER B 163 LYS B 182 1 20 HELIX 9 9 SER B 209 LEU B 218 1 10 HELIX 10 10 ASN B 237 PHE B 244 1 8 SHEET 1 A 7 ASN A 73 GLN A 74 0 SHEET 2 A 7 ALA A 104 SER A 107 -1 O SER A 107 N ASN A 73 SHEET 3 A 7 VAL A 48 VAL A 54 -1 N LEU A 51 O ALA A 104 SHEET 4 A 7 THR A 9 MET A 19 1 N MET A 13 O ILE A 50 SHEET 5 A 7 VAL A 299 SER A 304 -1 O ALA A 301 N VAL A 12 SHEET 6 A 7 TYR A 266 VAL A 271 -1 N LYS A 270 O GLU A 300 SHEET 7 A 7 SER A 224 GLY A 227 1 N SER A 224 O ILE A 267 SHEET 1 B 6 LYS A 88 GLY A 91 0 SHEET 2 B 6 ILE A 111 VAL A 118 1 O GLN A 116 N LEU A 90 SHEET 3 B 6 GLY A 132 LYS A 140 -1 O TYR A 135 N ILE A 115 SHEET 4 B 6 ARG A 143 HIS A 151 -1 O VAL A 145 N ILE A 138 SHEET 5 B 6 VAL A 190 ASP A 195 1 O LEU A 191 N HIS A 146 SHEET 6 B 6 ASP A 253 ALA A 257 -1 O ILE A 256 N ILE A 192 SHEET 1 C 2 TRP A 279 SER A 283 0 SHEET 2 C 2 GLN A 286 TYR A 290 -1 O GLN A 286 N SER A 283 SHEET 1 D 7 ASN B 73 GLN B 74 0 SHEET 2 D 7 ALA B 104 SER B 107 -1 O SER B 107 N ASN B 73 SHEET 3 D 7 VAL B 48 VAL B 54 -1 N LEU B 51 O ALA B 104 SHEET 4 D 7 THR B 9 MET B 19 1 N MET B 13 O ILE B 50 SHEET 5 D 7 VAL B 299 SER B 304 -1 O ALA B 301 N VAL B 12 SHEET 6 D 7 TYR B 266 VAL B 271 -1 N LYS B 270 O GLU B 300 SHEET 7 D 7 SER B 224 GLY B 227 1 N SER B 224 O ILE B 267 SHEET 1 E 6 LYS B 88 GLY B 91 0 SHEET 2 E 6 ILE B 111 VAL B 118 1 O GLN B 116 N LEU B 90 SHEET 3 E 6 GLY B 132 LYS B 140 -1 O TYR B 135 N ILE B 115 SHEET 4 E 6 ARG B 143 HIS B 151 -1 O VAL B 145 N ILE B 138 SHEET 5 E 6 VAL B 190 ASP B 195 1 O LEU B 191 N HIS B 146 SHEET 6 E 6 ASP B 253 ALA B 257 -1 O ILE B 256 N ILE B 192 SHEET 1 F 2 TRP B 279 SER B 283 0 SHEET 2 F 2 GLN B 286 TYR B 290 -1 O GLN B 286 N SER B 283 LINK OE1 GLU A 53 MG MG A 310 1555 1555 2.09 LINK O PHE A 55 MG MG A 311 1555 1555 2.12 LINK OD1 ASN A 57 MG MG A 311 1555 1555 2.36 LINK OE1 GLU A 99 MG MG A 311 1555 1555 1.90 LINK OD2 ASP A 100 MG MG A 311 1555 1555 2.12 LINK MG MG A 310 O HOH A 322 1555 1555 2.09 LINK MG MG A 310 O HOH A 326 1555 1555 2.20 LINK MG MG A 310 O HOH A 352 1555 1555 2.33 LINK MG MG A 310 O HOH A 367 1555 1555 2.07 LINK MG MG A 310 O HOH A 384 1555 1555 2.42 LINK MG MG A 311 O HOH A 330 1555 1555 2.21 LINK MG MG A 311 O HOH A 372 1555 1555 2.26 LINK OE1 GLU B 53 MG MG B 308 1555 1555 2.05 LINK O PHE B 55 MG MG B 309 1555 1555 2.14 LINK OD1 ASN B 57 MG MG B 309 1555 1555 2.29 LINK OE1 GLU B 99 MG MG B 309 1555 1555 1.89 LINK OD2 ASP B 100 MG MG B 309 1555 1555 2.23 LINK MG MG B 308 O HOH B 328 1555 1555 2.08 LINK MG MG B 308 O HOH B 334 1555 1555 2.05 LINK MG MG B 308 O HOH B 351 1555 1555 2.29 LINK MG MG B 308 O HOH B 353 1555 1555 2.33 LINK MG MG B 308 O HOH B 386 1555 1555 2.40 LINK MG MG B 309 O HOH B 383 1555 1555 2.19 LINK MG MG B 309 O HOH B 400 1555 1555 2.14 SITE 1 AC1 6 GLU B 53 HOH B 328 HOH B 334 HOH B 351 SITE 2 AC1 6 HOH B 353 HOH B 386 SITE 1 AC2 6 PHE B 55 ASN B 57 GLU B 99 ASP B 100 SITE 2 AC2 6 HOH B 383 HOH B 400 SITE 1 AC3 6 GLU A 53 HOH A 322 HOH A 326 HOH A 352 SITE 2 AC3 6 HOH A 367 HOH A 384 SITE 1 AC4 6 PHE A 55 ASN A 57 GLU A 99 ASP A 100 SITE 2 AC4 6 HOH A 330 HOH A 372 SITE 1 AC5 6 ALA A 40 ASP A 41 TYR A 42 LYS A 275 SITE 2 AC5 6 TYR A 293 HOH A 597 SITE 1 AC6 5 ASP B 41 TYR B 42 LYS B 275 TYR B 293 SITE 2 AC6 5 HOH B 813 SITE 1 AC7 10 TYR A 25 PRO A 26 ASN A 27 TRP A 28 SITE 2 AC7 10 TYR A 242 VAL A 281 SER A 283 TRP A 284 SITE 3 AC7 10 TYR A 288 TYR A 290 SITE 1 AC8 11 TYR B 25 PRO B 26 ASN B 27 TRP B 28 SITE 2 AC8 11 TYR B 242 VAL B 281 SER B 283 TRP B 284 SITE 3 AC8 11 TYR B 288 TYR B 290 HOH B 707 CRYST1 50.844 50.893 59.506 81.87 81.84 79.68 P 1 2 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 0.019668 -0.003583 -0.002409 0.00000 SCALE2 0.000000 0.019972 -0.002396 0.00000 SCALE3 0.000000 0.000000 0.017099 0.00000