HEADER HYDROLASE 18-NOV-10 3PN9 TITLE CRYSTAL STRUCTURE OF A PROLINE DIPEPTIDASE FROM STREPTOCOCCUS TITLE 2 PNEUMONIAE TIGR4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLINE DIPEPTIDASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 3.4.13.9; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: PEPQ, SP_1591; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG19 KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, MCSG, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.JOACHIMIAK,N.E.C.DUKE,G.CHHOR,S.CLANCY,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 2 26-SEP-12 3PN9 1 AUTHOR VERSN REVDAT 1 22-DEC-10 3PN9 0 JRNL AUTH A.JOACHIMIAK,N.E.C.DUKE,G.CHHOR,S.CLANCY, JRNL AUTH 2 MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) JRNL TITL CRYSTAL STRUCTURE OF A PROLINE DIPEPTIDASE FROM JRNL TITL 2 STREPTOCOCCUS PNEUMONIAE TIGR4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 99.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 88411 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4442 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5780 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 289 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4440 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 488 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35000 REMARK 3 B22 (A**2) : -0.35000 REMARK 3 B33 (A**2) : 0.70000 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): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.296 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4560 ; 0.037 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6201 ; 2.493 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 540 ; 6.516 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 213 ;42.086 ;24.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 798 ;15.686 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;16.888 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 712 ; 0.228 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3416 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2740 ; 1.884 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4490 ; 3.242 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1820 ; 4.569 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1711 ; 7.230 ; 4.500 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 : 1.40 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 REMARK 4 REMARK 4 3PN9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-10. REMARK 100 THE RCSB ID CODE IS RCSB062581. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940, 0.97937 REMARK 200 MONOCHROMATOR : SI-111 CHANNEL REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 168476 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 99.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : 0.09100 REMARK 200 FOR THE DATA SET : 38.2090 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : 0.80000 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: HKL-3000, MLPHARE, DM, SHELXD, RESOLVE, ARP/WARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS(0.1M, PH=8.5), LITHIUM SULFATE REMARK 280 (0.2M, PH=N/A), AMMONIUM SULFATE (2M, PH=N/A), TEMPERATURE 277K, REMARK 280 VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.67400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 59.03650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 59.03650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.33700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 59.03650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 59.03650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 139.01100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 59.03650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.03650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.33700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 59.03650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.03650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 139.01100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 92.67400 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 SER C -2 REMARK 465 ASN C -1 REMARK 465 SER D -2 REMARK 465 ASN D -1 REMARK 465 ALA D 0 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 HOH B 253 O HOH B 304 2.03 REMARK 500 O HOH D 158 O HOH D 272 2.14 REMARK 500 O HOH A 158 O HOH A 266 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 39 NH2 ARG C 130 5545 2.10 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 TYR A 29 CD1 TYR A 29 CE1 0.092 REMARK 500 GLU A 39 CB GLU A 39 CG 0.155 REMARK 500 GLU A 39 CG GLU A 39 CD 0.117 REMARK 500 VAL A 73 CB VAL A 73 CG1 0.148 REMARK 500 ALA A 98 CA ALA A 98 CB 0.137 REMARK 500 GLU A 120 CG GLU A 120 CD 0.093 REMARK 500 ALA B 19 CA ALA B 19 CB 0.134 REMARK 500 GLU B 39 CB GLU B 39 CG 0.153 REMARK 500 GLU C 39 CB GLU C 39 CG 0.140 REMARK 500 GLU C 39 CG GLU C 39 CD 0.098 REMARK 500 GLU C 120 CG GLU C 120 CD 0.091 REMARK 500 TYR D 29 CE2 TYR D 29 CD2 0.125 REMARK 500 GLU D 39 CB GLU D 39 CG 0.150 REMARK 500 VAL D 46 CB VAL D 46 CG1 0.139 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 LEU A 4 CB - CG - CD2 ANGL. DEV. = 16.4 DEGREES REMARK 500 TYR A 10 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 LYS B 3 CD - CE - NZ ANGL. DEV. = -19.1 DEGREES REMARK 500 LEU B 47 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG C 63 CG - CD - NE ANGL. DEV. = -14.3 DEGREES REMARK 500 ARG C 63 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG C 63 NE - CZ - NH1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG C 63 NE - CZ - NH2 ANGL. DEV. = -10.8 DEGREES REMARK 500 ASP D 17 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG D 132 NE - CZ - NH2 ANGL. DEV. = -4.0 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 HIS A 38 -108.07 47.15 REMARK 500 HIS B 38 -115.00 55.08 REMARK 500 HIS C 38 -117.88 45.53 REMARK 500 HIS D 38 -115.66 54.88 REMARK 500 GLN D 91 57.98 -90.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 134 LYS A 135 -141.55 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 SO4 A 136 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 136 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 136 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 136 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC63977.1 RELATED DB: TARGETDB DBREF 3PN9 A 1 135 UNP Q97PL5 Q97PL5_STRPN 1 135 DBREF 3PN9 B 1 135 UNP Q97PL5 Q97PL5_STRPN 1 135 DBREF 3PN9 C 1 135 UNP Q97PL5 Q97PL5_STRPN 1 135 DBREF 3PN9 D 1 135 UNP Q97PL5 Q97PL5_STRPN 1 135 SEQADV 3PN9 SER A -2 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ASN A -1 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ALA A 0 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 SER B -2 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ASN B -1 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ALA B 0 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 SER C -2 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ASN C -1 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ALA C 0 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 SER D -2 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ASN D -1 UNP Q97PL5 EXPRESSION TAG SEQADV 3PN9 ALA D 0 UNP Q97PL5 EXPRESSION TAG SEQRES 1 A 138 SER ASN ALA MSE SER LYS LEU GLN GLN ILE LEU THR TYR SEQRES 2 A 138 LEU GLU SER GLU LYS LEU ASP VAL ALA VAL VAL SER ASP SEQRES 3 A 138 PRO VAL THR ILE ASN TYR LEU THR GLY PHE TYR SER ASP SEQRES 4 A 138 PRO HIS GLU ARG GLN MSE PHE LEU PHE VAL LEU ALA ASP SEQRES 5 A 138 GLN GLU PRO LEU LEU PHE VAL PRO ALA LEU GLU VAL GLU SEQRES 6 A 138 ARG ALA SER SER THR VAL SER PHE PRO VAL VAL GLY TYR SEQRES 7 A 138 VAL ASP SER GLU ASN PRO TRP GLN LYS ILE LYS HIS ALA SEQRES 8 A 138 LEU PRO GLN LEU ASP PHE LYS ARG VAL ALA VAL GLU PHE SEQRES 9 A 138 ASP ASN LEU ILE LEU THR LYS TYR HIS GLY LEU LYS THR SEQRES 10 A 138 VAL PHE GLU THR ALA GLU PHE ASP ASN LEU THR PRO ARG SEQRES 11 A 138 ILE GLN ARG MSE ARG LEU ILE LYS SEQRES 1 B 138 SER ASN ALA MSE SER LYS LEU GLN GLN ILE LEU THR TYR SEQRES 2 B 138 LEU GLU SER GLU LYS LEU ASP VAL ALA VAL VAL SER ASP SEQRES 3 B 138 PRO VAL THR ILE ASN TYR LEU THR GLY PHE TYR SER ASP SEQRES 4 B 138 PRO HIS GLU ARG GLN MSE PHE LEU PHE VAL LEU ALA ASP SEQRES 5 B 138 GLN GLU PRO LEU LEU PHE VAL PRO ALA LEU GLU VAL GLU SEQRES 6 B 138 ARG ALA SER SER THR VAL SER PHE PRO VAL VAL GLY TYR SEQRES 7 B 138 VAL ASP SER GLU ASN PRO TRP GLN LYS ILE LYS HIS ALA SEQRES 8 B 138 LEU PRO GLN LEU ASP PHE LYS ARG VAL ALA VAL GLU PHE SEQRES 9 B 138 ASP ASN LEU ILE LEU THR LYS TYR HIS GLY LEU LYS THR SEQRES 10 B 138 VAL PHE GLU THR ALA GLU PHE ASP ASN LEU THR PRO ARG SEQRES 11 B 138 ILE GLN ARG MSE ARG LEU ILE LYS SEQRES 1 C 138 SER ASN ALA MSE SER LYS LEU GLN GLN ILE LEU THR TYR SEQRES 2 C 138 LEU GLU SER GLU LYS LEU ASP VAL ALA VAL VAL SER ASP SEQRES 3 C 138 PRO VAL THR ILE ASN TYR LEU THR GLY PHE TYR SER ASP SEQRES 4 C 138 PRO HIS GLU ARG GLN MSE PHE LEU PHE VAL LEU ALA ASP SEQRES 5 C 138 GLN GLU PRO LEU LEU PHE VAL PRO ALA LEU GLU VAL GLU SEQRES 6 C 138 ARG ALA SER SER THR VAL SER PHE PRO VAL VAL GLY TYR SEQRES 7 C 138 VAL ASP SER GLU ASN PRO TRP GLN LYS ILE LYS HIS ALA SEQRES 8 C 138 LEU PRO GLN LEU ASP PHE LYS ARG VAL ALA VAL GLU PHE SEQRES 9 C 138 ASP ASN LEU ILE LEU THR LYS TYR HIS GLY LEU LYS THR SEQRES 10 C 138 VAL PHE GLU THR ALA GLU PHE ASP ASN LEU THR PRO ARG SEQRES 11 C 138 ILE GLN ARG MSE ARG LEU ILE LYS SEQRES 1 D 138 SER ASN ALA MSE SER LYS LEU GLN GLN ILE LEU THR TYR SEQRES 2 D 138 LEU GLU SER GLU LYS LEU ASP VAL ALA VAL VAL SER ASP SEQRES 3 D 138 PRO VAL THR ILE ASN TYR LEU THR GLY PHE TYR SER ASP SEQRES 4 D 138 PRO HIS GLU ARG GLN MSE PHE LEU PHE VAL LEU ALA ASP SEQRES 5 D 138 GLN GLU PRO LEU LEU PHE VAL PRO ALA LEU GLU VAL GLU SEQRES 6 D 138 ARG ALA SER SER THR VAL SER PHE PRO VAL VAL GLY TYR SEQRES 7 D 138 VAL ASP SER GLU ASN PRO TRP GLN LYS ILE LYS HIS ALA SEQRES 8 D 138 LEU PRO GLN LEU ASP PHE LYS ARG VAL ALA VAL GLU PHE SEQRES 9 D 138 ASP ASN LEU ILE LEU THR LYS TYR HIS GLY LEU LYS THR SEQRES 10 D 138 VAL PHE GLU THR ALA GLU PHE ASP ASN LEU THR PRO ARG SEQRES 11 D 138 ILE GLN ARG MSE ARG LEU ILE LYS MODRES 3PN9 MSE A 1 MET SELENOMETHIONINE MODRES 3PN9 MSE A 42 MET SELENOMETHIONINE MODRES 3PN9 MSE A 131 MET SELENOMETHIONINE MODRES 3PN9 MSE B 1 MET SELENOMETHIONINE MODRES 3PN9 MSE B 42 MET SELENOMETHIONINE MODRES 3PN9 MSE B 131 MET SELENOMETHIONINE MODRES 3PN9 MSE C 1 MET SELENOMETHIONINE MODRES 3PN9 MSE C 42 MET SELENOMETHIONINE MODRES 3PN9 MSE C 131 MET SELENOMETHIONINE MODRES 3PN9 MSE D 1 MET SELENOMETHIONINE MODRES 3PN9 MSE D 42 MET SELENOMETHIONINE MODRES 3PN9 MSE D 131 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 42 8 HET MSE A 131 8 HET MSE B 1 8 HET MSE B 42 8 HET MSE B 131 8 HET MSE C 1 8 HET MSE C 42 8 HET MSE C 131 8 HET MSE D 1 8 HET MSE D 42 8 HET MSE D 131 8 HET SO4 A 136 5 HET SO4 B 136 5 HET SO4 C 136 5 HET SO4 D 136 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 HOH *488(H2 O) HELIX 1 1 SER A 2 LYS A 15 1 14 HELIX 2 2 ASP A 23 GLY A 32 1 10 HELIX 3 3 GLU A 60 VAL A 68 1 9 HELIX 4 4 ASN A 80 LEU A 89 1 10 HELIX 5 5 ILE A 105 PHE A 116 1 12 HELIX 6 6 LEU A 124 ARG A 132 1 9 HELIX 7 7 SER B 2 GLU B 14 1 13 HELIX 8 8 ASP B 23 GLY B 32 1 10 HELIX 9 9 GLU B 60 VAL B 68 1 9 HELIX 10 10 ASN B 80 LEU B 89 1 10 HELIX 11 11 ILE B 105 PHE B 116 1 12 HELIX 12 12 LEU B 124 ARG B 132 1 9 HELIX 13 13 SER C 2 GLU C 14 1 13 HELIX 14 14 ASP C 23 GLY C 32 1 10 HELIX 15 15 GLU C 60 VAL C 68 1 9 HELIX 16 16 ASN C 80 LEU C 89 1 10 HELIX 17 17 ILE C 105 PHE C 116 1 12 HELIX 18 18 LEU C 124 ARG C 132 1 9 HELIX 19 19 SER D 2 GLU D 14 1 13 HELIX 20 20 ASP D 23 GLY D 32 1 10 HELIX 21 21 GLU D 60 VAL D 68 1 9 HELIX 22 22 ASN D 80 LEU D 89 1 10 HELIX 23 23 ILE D 105 PHE D 116 1 12 HELIX 24 24 LEU D 124 ARG D 132 1 9 SHEET 1 A 6 VAL A 72 TYR A 75 0 SHEET 2 A 6 LEU A 53 PRO A 57 1 N VAL A 56 O VAL A 73 SHEET 3 A 6 PHE A 43 LEU A 47 -1 N PHE A 43 O PHE A 55 SHEET 4 A 6 VAL A 18 VAL A 21 -1 N ALA A 19 O VAL A 46 SHEET 5 A 6 ARG A 96 VAL A 99 1 O ALA A 98 N VAL A 20 SHEET 6 A 6 GLU A 120 ASN A 123 1 O ASP A 122 N VAL A 97 SHEET 1 B 6 VAL B 72 TYR B 75 0 SHEET 2 B 6 LEU B 53 PRO B 57 1 N VAL B 56 O VAL B 73 SHEET 3 B 6 PHE B 43 LEU B 47 -1 N PHE B 43 O PHE B 55 SHEET 4 B 6 VAL B 18 VAL B 21 -1 N VAL B 21 O LEU B 44 SHEET 5 B 6 ARG B 96 VAL B 99 1 O ALA B 98 N VAL B 20 SHEET 6 B 6 GLU B 120 ASN B 123 1 O ASP B 122 N VAL B 99 SHEET 1 C 6 VAL C 72 TYR C 75 0 SHEET 2 C 6 LEU C 53 PRO C 57 1 N VAL C 56 O VAL C 73 SHEET 3 C 6 PHE C 43 LEU C 47 -1 N PHE C 45 O LEU C 53 SHEET 4 C 6 VAL C 18 VAL C 21 -1 N VAL C 21 O LEU C 44 SHEET 5 C 6 ARG C 96 VAL C 99 1 O ALA C 98 N VAL C 20 SHEET 6 C 6 GLU C 120 ASN C 123 1 O GLU C 120 N VAL C 97 SHEET 1 D 6 VAL D 72 TYR D 75 0 SHEET 2 D 6 LEU D 53 PRO D 57 1 N VAL D 56 O VAL D 73 SHEET 3 D 6 PHE D 43 LEU D 47 -1 N PHE D 43 O PHE D 55 SHEET 4 D 6 VAL D 18 VAL D 21 -1 N ALA D 19 O VAL D 46 SHEET 5 D 6 ARG D 96 VAL D 99 1 O ALA D 98 N VAL D 20 SHEET 6 D 6 GLU D 120 ASN D 123 1 O ASP D 122 N VAL D 99 LINK C ALA A 0 N MSE A 1 1555 1555 1.32 LINK C MSE A 1 N SER A 2 1555 1555 1.32 LINK C GLN A 41 N MSE A 42 1555 1555 1.33 LINK C MSE A 42 N PHE A 43 1555 1555 1.33 LINK C ARG A 130 N MSE A 131 1555 1555 1.36 LINK C MSE A 131 N ARG A 132 1555 1555 1.32 LINK C MSE B 1 N SER B 2 1555 1555 1.36 LINK C GLN B 41 N MSE B 42 1555 1555 1.34 LINK C MSE B 42 N PHE B 43 1555 1555 1.32 LINK C ARG B 130 N MSE B 131 1555 1555 1.35 LINK C MSE B 131 N ARG B 132 1555 1555 1.32 LINK C ALA C 0 N MSE C 1 1555 1555 1.35 LINK C MSE C 1 N SER C 2 1555 1555 1.35 LINK C GLN C 41 N MSE C 42 1555 1555 1.33 LINK C MSE C 42 N PHE C 43 1555 1555 1.34 LINK C ARG C 130 N MSE C 131 1555 1555 1.35 LINK C MSE C 131 N ARG C 132 1555 1555 1.33 LINK C MSE D 1 N SER D 2 1555 1555 1.35 LINK C GLN D 41 N MSE D 42 1555 1555 1.36 LINK C MSE D 42 N PHE D 43 1555 1555 1.33 LINK C ARG D 130 N MSE D 131 1555 1555 1.33 LINK C MSE D 131 N ARG D 132 1555 1555 1.33 SITE 1 AC1 3 SER A 2 LYS A 3 HOH A 320 SITE 1 AC2 4 SER B 2 LYS B 3 HOH B 362 HOH B 363 SITE 1 AC3 3 SER C 2 LYS C 3 HOH C 178 SITE 1 AC4 4 SER D 2 LYS D 3 HOH D 422 HOH D 423 CRYST1 118.073 118.073 185.348 90.00 90.00 90.00 P 41 21 2 32 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 0.008470 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005390 0.00000