HEADER VIRAL PROTEIN 20-FEB-24 8S3M TITLE LYSTT72, A LYTIC ENDOPEPTIDASE FROM THERMUS THERMOPHILUS MAT72 PHAGE TITLE 2 VB_TT72 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYTIC ENDOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.24.32; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GAMMA-D-GLU-M-A2PM-L-LYS-L-ARG; COMPND 8 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS PHAGE TT72; SOURCE 3 ORGANISM_TAXID: 2978976; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: BL21(DE3)[PRARE]; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 9 ORGANISM_TAXID: 469008 KEYWDS ENDOPEPTIDASE, METALLOPROTEIN, THERMOSTABILITY, BACTERIOPHAGE, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.RYPNIEWSKI,K.BINIEK-ANTOSIAK,M.BEJGER REVDAT 2 17-SEP-25 8S3M 1 JRNL REVDAT 1 05-MAR-25 8S3M 0 JRNL AUTH S.DORAWA,K.BINIEK-ANTOSIAK,M.BEJGER,A.K.KACZOROWSKA, JRNL AUTH 2 K.CIUCHCINSKI,A.GODLEWSKA,M.PLOTKA,G.O.HREGGVIDSSON, JRNL AUTH 3 L.DZIEWIT,T.KACZOROWSKI,W.RYPNIEWSKI JRNL TITL CRYSTAL STRUCTURE, ENZYMATIC AND THERMODYNAMIC PROPERTIES OF JRNL TITL 2 THE THERMUS THERMOPHILUS PHAGE TT72 LYTIC ENDOPEPTIDASE WITH JRNL TITL 3 UNIQUE STRUCTURAL SIGNATURES OF THERMAL ADAPTATION. JRNL REF J.STRUCT.BIOL. V. 217 08230 2025 JRNL REFN ESSN 1095-8657 JRNL PMID 40580998 JRNL DOI 10.1016/J.JSB.2025.108230 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 17755 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.238 REMARK 3 FREE R VALUE TEST SET COUNT : 930 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1156 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3470 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2837 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.19200 REMARK 3 B22 (A**2) : -1.16700 REMARK 3 B33 (A**2) : -3.02500 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): 0.316 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.219 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.401 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2923 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2671 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3965 ; 1.641 ; 1.813 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6152 ; 0.571 ; 1.765 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 344 ; 7.771 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 13 ; 7.360 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;17.887 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 421 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3437 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 729 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 606 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 46 ; 0.236 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1461 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 122 ; 0.184 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.142 ; 0.200 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): 1382 ; 3.717 ; 3.982 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1382 ; 3.717 ; 3.981 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1724 ; 5.648 ; 7.143 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1725 ; 5.652 ; 7.145 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1541 ; 4.410 ; 4.438 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1538 ; 4.389 ; 4.431 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2241 ; 6.849 ; 7.948 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2242 ; 6.847 ; 7.950 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 BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8S3M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-23 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7749 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : FOCUSSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17755 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.198 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.24300 REMARK 200 FOR THE DATA SET : 8.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.47800 REMARK 200 FOR SHELL : 1.650 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 (%): 42.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% V/V PEG 500 MME, 10% W/V PEG REMARK 280 20000, 30 MM SODIUM NITRATE, 30 MM SODIUM PHOSPHATE DIBASIC, 30 REMARK 280 MM AMMONIUM SULFATE, 0.1 M 6.5 IMIDAZOLE/MES MONOHYDRATE (ACID) REMARK 280 AT PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 22.06650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.67100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.49250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.67100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.06650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.49250 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: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 1 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 ARG C 4 NE ARG C 4 CZ 0.082 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG C 4 NE - CZ - NH1 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG C 4 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 GLN A 3 108.06 177.60 REMARK 500 SER A 33 156.90 -36.64 REMARK 500 ASN A 90 -70.89 -129.05 REMARK 500 ALA A 92 18.52 59.20 REMARK 500 PRO A 116 33.02 -84.26 REMARK 500 TYR A 122 -70.93 -101.21 REMARK 500 GLU A 125 -123.03 57.62 REMARK 500 ALA A 144 143.19 -170.45 REMARK 500 ALA A 151 -102.55 67.86 REMARK 500 SER A 156 -154.98 62.34 REMARK 500 CYS A 165 74.18 -153.32 REMARK 500 GLN A 166 72.90 57.82 REMARK 500 HIS A 176 41.88 72.90 REMARK 500 PRO A 225 154.39 -44.08 REMARK 500 PRO A 328 -76.11 -25.55 REMARK 500 PHE A 330 -52.03 -165.29 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 74 0.08 SIDE CHAIN 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 115 NE2 REMARK 620 2 ASP A 119 OD1 101.7 REMARK 620 3 ASP A 119 OD2 80.9 54.8 REMARK 620 4 HIS A 208 ND1 110.2 95.9 150.7 REMARK 620 5 PO4 A 402 O3 146.7 82.6 74.9 102.0 REMARK 620 6 PO4 A 402 O4 94.9 143.4 96.9 108.7 66.3 REMARK 620 N 1 2 3 4 5 DBREF 8S3M A 1 346 PDB 8S3M 8S3M 1 346 DBREF 8S3M C 1 4 PDB 8S3M 8S3M 1 4 SEQRES 1 A 346 MET GLU GLN LYS VAL TYR PHE PRO ILE ASN CYS SER LEU SEQRES 2 A 346 SER PRO ILE THR ILE THR THR ASN TYR GLY GLU PRO TYR SEQRES 3 A 346 PRO ASN GLN LYS PHE PHE SER LEU ARG GLU GLN ARG ILE SEQRES 4 A 346 LEU PHE ASP ILE ALA SER LEU ILE ARG SER TYR GLU SER SEQRES 5 A 346 ASN TYR SER SER PHE LYS GLN ASN TYR PRO ASN LEU PRO SEQRES 6 A 346 GLN ASN LEU SER SER ILE THR ASN ARG ILE LEU LEU LEU SEQRES 7 A 346 GLU PHE ILE VAL ASN THR ASN PRO GLN LYS LEU ASN PHE SEQRES 8 A 346 ALA ARG SER LYS ILE LEU SER ASP ARG SER LYS LEU ILE SEQRES 9 A 346 ASP LYS SER ASN PHE LYS TYR ILE SER PHE HIS PRO GLY SEQRES 10 A 346 VAL ASP ILE ASN TYR GLY SER GLU ASN GLN ASP PHE GLY SEQRES 11 A 346 LEU PRO VAL TYR ALA VAL THR ASP GLY VAL VAL ILE ASN SEQRES 12 A 346 ALA SER ARG HIS PHE CYS SER ALA SER CYS ASP CYS SER SEQRES 13 A 346 GLY PHE VAL ALA VAL GLU HIS ARG CYS GLN ASN LYS ILE SEQRES 14 A 346 PHE TYR ALA LEU TYR GLY HIS VAL VAL PRO GLU ALA ASN SEQRES 15 A 346 ILE GLY LYS LYS VAL LYS ALA GLY GLU ARG ILE ALA SER SEQRES 16 A 346 ILE GLY GLU TYR LYS CYS ASN SER THR SER HIS LEU HIS SEQRES 17 A 346 LEU GLU ILE THR LEU LYS ASN ILE TYR SER ASN PHE PRO SEQRES 18 A 346 LYS ASN TYR PRO ARG ASN MET TYR LYS ASP LYS GLY LEU SEQRES 19 A 346 ASN LEU ALA TYR ILE ALA ALA ILE LEU TYR ASP ILE LEU SEQRES 20 A 346 ASN THR THR THR SER SER THR GLN TYR CYS LEU ASP TYR SEQRES 21 A 346 LYS TYR TYR ILE ASN SER PHE MET ASP PRO ASN GLU SER SEQRES 22 A 346 TRP ASN PHE PHE GLY LYS ASN ASN PRO TYR THR GLN ALA SEQRES 23 A 346 THR SER ASP GLU VAL PHE TYR GLY GLY SER TYR ALA LYS SEQRES 24 A 346 TYR TYR GLY TYR ILE GLU PRO LEU ASN PHE LEU ARG SER SEQRES 25 A 346 PHE GLY GLN ASN LYS VAL TYR SER PRO VAL THR GLN SER SEQRES 26 A 346 LEU CYS PRO ASN PHE ASN THR ARG ARG SER LEU THR PRO SEQRES 27 A 346 MET LYS ILE CYS PHE ALA VAL GLN SEQRES 1 C 4 FGA API LYS ARG HET FGA C 1 8 HET API C 2 12 HET ZN A 401 1 HET PO4 A 402 5 HET PO4 C 101 5 HETNAM FGA GAMMA-D-GLUTAMIC ACID HETNAM API 2,6-DIAMINOPIMELIC ACID HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION HETSYN FGA D-GLUTAMIC ACID FORMUL 2 FGA C5 H9 N O4 FORMUL 2 API C7 H14 N2 O4 FORMUL 3 ZN ZN 2+ FORMUL 4 PO4 2(O4 P 3-) FORMUL 6 HOH *65(H2 O) HELIX 1 AA1 TYR A 26 GLN A 29 5 4 HELIX 2 AA2 SER A 33 ASN A 53 1 21 HELIX 3 AA3 ASN A 53 TYR A 61 1 9 HELIX 4 AA4 SER A 70 THR A 84 1 15 HELIX 5 AA5 ASN A 85 LEU A 89 5 5 HELIX 6 AA6 ALA A 92 ILE A 104 1 13 HELIX 7 AA7 ASP A 105 SER A 107 5 3 HELIX 8 AA8 ARG A 226 LYS A 230 5 5 HELIX 9 AA9 LEU A 236 LEU A 243 1 8 HELIX 10 AB1 LEU A 243 ASN A 248 1 6 HELIX 11 AB2 TYR A 260 ILE A 264 1 5 HELIX 12 AB3 ASN A 281 SER A 288 1 8 HELIX 13 AB4 GLY A 295 GLY A 302 1 8 HELIX 14 AB5 GLU A 305 GLY A 314 1 10 SHEET 1 AA1 2 VAL A 5 TYR A 6 0 SHEET 2 AA1 2 VAL A 318 TYR A 319 1 O TYR A 319 N VAL A 5 SHEET 1 AA2 7 THR A 17 THR A 20 0 SHEET 2 AA2 7 VAL A 118 ASN A 121 -1 O ASN A 121 N THR A 17 SHEET 3 AA2 7 LEU A 207 THR A 212 -1 O LEU A 209 N VAL A 118 SHEET 4 AA2 7 ILE A 169 PRO A 179 -1 N GLY A 175 O HIS A 208 SHEET 5 AA2 7 GLY A 157 ARG A 164 -1 N VAL A 159 O TYR A 174 SHEET 6 AA2 7 GLY A 139 SER A 145 -1 N ASN A 143 O ALA A 160 SHEET 7 AA2 7 LYS A 186 VAL A 187 -1 O VAL A 187 N GLY A 139 SHEET 1 AA3 5 PRO A 132 TYR A 134 0 SHEET 2 AA3 5 ARG A 192 ILE A 196 -1 O ALA A 194 N VAL A 133 SHEET 3 AA3 5 ILE A 169 PRO A 179 -1 N VAL A 178 O SER A 195 SHEET 4 AA3 5 LEU A 207 THR A 212 -1 O HIS A 208 N GLY A 175 SHEET 5 AA3 5 TYR A 303 ILE A 304 -1 O ILE A 304 N ILE A 211 SHEET 1 AA4 3 PHE A 31 PHE A 32 0 SHEET 2 AA4 3 LYS A 340 VAL A 345 1 O ALA A 344 N PHE A 32 SHEET 3 AA4 3 GLN A 255 ASP A 259 -1 N LEU A 258 O ILE A 341 SHEET 1 AA5 3 PHE A 109 LYS A 110 0 SHEET 2 AA5 3 GLY A 233 ASN A 235 -1 O LEU A 234 N LYS A 110 SHEET 3 AA5 3 PHE A 267 MET A 268 -1 O MET A 268 N GLY A 233 SSBOND 1 CYS A 11 CYS A 327 1555 1555 2.29 SSBOND 2 CYS A 149 CYS A 155 1555 1555 2.11 SSBOND 3 CYS A 153 CYS A 201 1555 1555 2.03 SSBOND 4 CYS A 257 CYS A 342 1555 1555 2.12 LINK CD FGA C 1 N API C 2 1555 1555 1.34 LINK C API C 2 N LYS C 3 1555 1555 1.34 LINK NE2 HIS A 115 ZN ZN A 401 1555 1555 1.82 LINK OD1 ASP A 119 ZN ZN A 401 1555 1555 1.99 LINK OD2 ASP A 119 ZN ZN A 401 1555 1555 2.60 LINK ND1 HIS A 208 ZN ZN A 401 1555 1555 2.02 LINK ZN ZN A 401 O3 PO4 A 402 1555 1555 2.31 LINK ZN ZN A 401 O4 PO4 A 402 1555 1555 2.16 CISPEP 1 SER A 14 PRO A 15 0 -5.32 CISPEP 2 PHE A 220 PRO A 221 0 -4.79 CRYST1 44.133 60.985 125.342 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 0.022659 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016397 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007978 0.00000 CONECT 86 2641 CONECT 950 2840 CONECT 975 2840 CONECT 976 2840 CONECT 1207 1244 CONECT 1230 1601 CONECT 1244 1207 CONECT 1601 1230 CONECT 1653 2840 CONECT 2056 2763 CONECT 2641 86 CONECT 2763 2056 CONECT 2798 2799 CONECT 2799 2798 2800 2802 CONECT 2800 2799 2801 CONECT 2801 2800 CONECT 2802 2799 2803 CONECT 2803 2802 2804 CONECT 2804 2803 2805 2816 CONECT 2805 2804 CONECT 2806 2807 2813 2818 CONECT 2807 2806 2808 2816 CONECT 2808 2807 2809 CONECT 2809 2808 2810 CONECT 2810 2809 2811 CONECT 2811 2810 2812 2817 CONECT 2812 2811 2814 2815 CONECT 2813 2806 CONECT 2814 2812 CONECT 2815 2812 CONECT 2816 2804 2807 CONECT 2817 2811 CONECT 2818 2806 CONECT 2840 950 975 976 1653 CONECT 2840 2844 2845 CONECT 2841 2842 2843 2844 2845 CONECT 2842 2841 CONECT 2843 2841 CONECT 2844 2840 2841 CONECT 2845 2840 2841 CONECT 2846 2847 2848 2849 2850 CONECT 2847 2846 CONECT 2848 2846 CONECT 2849 2846 CONECT 2850 2846 MASTER 352 0 5 14 20 0 0 6 2913 2 45 28 END