HEADER HYDROLASE 05-FEB-15 4Y04 TITLE CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE 11 (DPP11) FROM TITLE 2 PORPHYROMONAS GINGIVALIS (SPACE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE S46; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PORPHYROMONAS GINGIVALIS; SOURCE 3 ORGANISM_TAXID: 837; SOURCE 4 GENE: EG14_04230; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) GOLD; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS SPACE, WT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SAKAMOTO,Y.SUZUKI,I.IIZUKA,C.TATEOKA,S.ROPPONGI,M.FUJIMOTO,K.INAKA, AUTHOR 2 H.TANAKA,M.YAMADA,K.OHTA,T.NONAKA,W.OGASAWARA,N.TANAKA REVDAT 3 08-NOV-23 4Y04 1 REMARK REVDAT 2 05-FEB-20 4Y04 1 SOURCE REMARK REVDAT 1 15-JUL-15 4Y04 0 JRNL AUTH Y.SAKAMOTO,Y.SUZUKI,I.IIZUKA,C.TATEOKA,S.ROPPONGI, JRNL AUTH 2 M.FUJIMOTO,K.INAKA,H.TANAKA,M.YAMADA,K.OHTA,H.GOUDA, JRNL AUTH 3 T.NONAKA,W.OGASAWARA,N.TANAKA JRNL TITL STRUCTURAL AND MUTATIONAL ANALYSES OF DIPEPTIDYL PEPTIDASE JRNL TITL 2 11 FROM PORPHYROMONAS GINGIVALIS REVEAL THE MOLECULAR BASIS JRNL TITL 3 FOR STRICT SUBSTRATE SPECIFICITY. JRNL REF SCI REP V. 5 11151 2015 JRNL REFN ESSN 2045-2322 JRNL PMID 26057589 JRNL DOI 10.1038/SREP11151 REMARK 2 REMARK 2 RESOLUTION. 1.66 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 100599 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5266 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) : 1.66 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7398 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 367 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5522 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 696 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.78000 REMARK 3 B22 (A**2) : -1.10000 REMARK 3 B33 (A**2) : 2.88000 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.548 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5664 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5348 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7649 ; 1.955 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12294 ; 1.126 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 687 ; 7.453 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 286 ;33.089 ;23.776 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 988 ;14.047 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;18.735 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 800 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6451 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1343 ; 0.002 ; 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): 2751 ; 2.768 ; 2.949 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2750 ; 2.767 ; 2.948 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3437 ; 3.617 ; 4.411 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3438 ; 3.618 ; 4.412 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2913 ; 3.831 ; 3.351 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2913 ; 3.830 ; 3.351 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4213 ; 5.473 ; 4.859 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7233 ; 6.892 ;25.481 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6872 ; 6.712 ;24.770 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 4Y04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105914 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4Y01 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRI-POTASSIUM CITRATE, PEG 8000 REMARK 280 CRYSTALLISATION UNDER MICRO GRAVITY AT ISS KIBO., LIQUID REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 87.65500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 87.65500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 49.57000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.64000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.57000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.64000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 87.65500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.57000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.64000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 87.65500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.57000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.64000 REMARK 290 SMTRY3 8 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 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 87.65500 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 465 LYS A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LEU A 5 REMARK 465 LEU A 6 REMARK 465 LEU A 7 REMARK 465 PRO A 8 REMARK 465 LEU A 9 REMARK 465 PHE A 10 REMARK 465 ALA A 11 REMARK 465 ALA A 12 REMARK 465 LEU A 13 REMARK 465 CYS A 14 REMARK 465 LEU A 15 REMARK 465 SER A 16 REMARK 465 GLN A 17 REMARK 465 ILE A 18 REMARK 465 ALA A 19 REMARK 465 HIS A 20 REMARK 465 ALA A 21 REMARK 465 ASP A 416 REMARK 465 GLU A 417 REMARK 465 THR A 418 REMARK 465 LYS A 419 REMARK 465 ALA A 420 REMARK 465 LEU A 421 REMARK 465 GLN A 422 REMARK 465 GLY A 423 REMARK 465 ASN A 424 REMARK 465 ASP A 425 REMARK 465 ALA A 426 REMARK 465 SER A 427 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 NH1 ARG A 673 O HOH A 1588 1.88 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 O HOH A 981 O HOH A 981 3555 1.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 161 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 351 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 351 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 392 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 392 NE - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 MET A 396 CG - SD - CE ANGL. DEV. = -10.7 DEGREES REMARK 500 ASP A 453 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 498 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 551 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 551 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 590 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 590 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 632 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 673 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 673 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 690 NE - CZ - NH1 ANGL. DEV. = 3.4 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 GLU A 98 -43.78 159.54 REMARK 500 ASN A 167 -11.67 72.70 REMARK 500 ASN A 172 83.49 -151.99 REMARK 500 ASN A 267 -1.50 75.66 REMARK 500 ILE A 294 -71.96 -109.50 REMARK 500 ILE A 401 -58.04 -128.51 REMARK 500 THR A 414 140.01 -179.60 REMARK 500 ARG A 429 145.86 -173.14 REMARK 500 LYS A 430 -47.70 88.91 REMARK 500 ALA A 512 -120.57 19.95 REMARK 500 GLU A 517 -92.27 91.29 REMARK 500 ASN A 574 42.47 -152.97 REMARK 500 VAL A 642 -61.94 -124.62 REMARK 500 TYR A 688 -32.52 -130.13 REMARK 500 CYS A 709 65.03 -103.39 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 PRO A 413 THR A 414 112.45 REMARK 500 ARG A 429 LYS A 430 40.11 REMARK 500 VAL A 516 GLU A 517 33.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1131 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A1342 DISTANCE = 7.41 ANGSTROMS 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 K A 801 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 218 OD1 REMARK 620 2 ASP A 672 OD1 122.5 REMARK 620 3 ASP A 672 OD2 80.3 42.8 REMARK 620 4 HOH A1583 O 166.3 56.0 95.2 REMARK 620 5 HOH A1587 O 87.5 147.8 156.8 92.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 278 O REMARK 620 2 THR A 278 OG1 57.2 REMARK 620 3 THR A 651 OG1 92.9 145.1 REMARK 620 4 ASP A 681 OD2 97.2 125.8 70.7 REMARK 620 5 HOH A1059 O 82.6 72.9 86.9 157.5 REMARK 620 6 HOH A1429 O 155.7 126.4 73.3 96.8 76.9 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 K A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 803 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XZY RELATED DB: PDB REMARK 900 RELATED ID: 4Y01 RELATED DB: PDB REMARK 900 RELATED ID: 4Y02 RELATED DB: PDB REMARK 900 RELATED ID: 4Y06 RELATED DB: PDB DBREF1 4Y04 A 1 720 UNP A0A076NW73_PORGN DBREF2 4Y04 A A0A076NW73 1 720 SEQRES 1 A 720 MET LYS LYS ARG LEU LEU LEU PRO LEU PHE ALA ALA LEU SEQRES 2 A 720 CYS LEU SER GLN ILE ALA HIS ALA ASP GLU GLY MET TRP SEQRES 3 A 720 LEU MET GLN GLN LEU GLY ARG LYS TYR ALA GLN MET LYS SEQRES 4 A 720 GLU ARG GLY LEU LYS MET LYS GLU TYR ASP LEU TYR ASN SEQRES 5 A 720 PRO ASN GLY THR SER LEU LYS ASP ALA VAL VAL LEU PHE SEQRES 6 A 720 ASP GLY GLY CYS THR GLY GLU VAL VAL SER ASP ARG GLY SEQRES 7 A 720 LEU VAL LEU THR ASN HIS HIS CYS GLY TYR ASP MET ILE SEQRES 8 A 720 GLN ALA HIS SER THR LEU GLU HIS ASN TYR LEU GLU ASN SEQRES 9 A 720 GLY PHE TRP ALA MET ARG GLU ALA ASP GLU LEU PRO ASN SEQRES 10 A 720 LYS ASP ILE SER VAL VAL PHE ILE ASP LYS ILE GLU ASP SEQRES 11 A 720 VAL THR ASP TYR VAL LYS LYS GLU LEU LYS ALA ILE LYS SEQRES 12 A 720 ASP PRO ASN SER MET ASP TYR LEU SER PRO LYS TYR LEU SEQRES 13 A 720 GLN LYS LEU ALA ASP LYS LYS ALA GLY LYS ASN PHE SER SEQRES 14 A 720 ALA LYS ASN PRO GLY LEU SER VAL GLU ILE LYS ALA PHE SEQRES 15 A 720 TYR GLY GLY ASN LEU TYR LEU MET PHE THR LYS LYS THR SEQRES 16 A 720 TYR THR ASP VAL ARG LEU VAL GLY ALA PRO PRO SER SER SEQRES 17 A 720 ILE GLY LYS PHE GLY ALA ASP THR ASP ASN TRP ILE TRP SEQRES 18 A 720 PRO ARG HIS THR GLY ASP PHE SER ILE PHE ARG ILE TYR SEQRES 19 A 720 ALA ASP LYS ASN GLY ASN PRO ALA PRO TYR SER GLU ASP SEQRES 20 A 720 ASN VAL PRO LEU LYS PRO LYS ARG PHE PHE ASN ILE SER SEQRES 21 A 720 LEU GLY GLY VAL GLN GLU ASN ASP TYR ALA MET ILE MET SEQRES 22 A 720 GLY PHE PRO GLY THR THR HIS ARG TYR PHE THR ALA SER SEQRES 23 A 720 GLU VAL ASP GLU TRP LYS SER ILE ASP ASN ASP ILE ARG SEQRES 24 A 720 ILE ARG MET ARG ASP ILE ARG GLN GLY VAL MET LEU ARG SEQRES 25 A 720 GLU MET LEU ALA ASP PRO GLN ILE LYS ILE MET TYR SER SEQRES 26 A 720 ALA LYS TYR ALA ALA SER GLN ASN ALA TYR LYS ARG ALA SEQRES 27 A 720 ILE GLY ALA ASN TRP ALA ILE LYS THR ARG GLY LEU ARG SEQRES 28 A 720 GLN ASN LYS GLN ALA MET GLN ASP ARG LEU ILE ALA TRP SEQRES 29 A 720 GLY ALA LYS GLN GLY THR PRO ARG TYR GLU GLU ALA VAL SEQRES 30 A 720 HIS GLU ILE ASP ALA THR VAL ALA LYS ARG ALA ASP LEU SEQRES 31 A 720 ARG ARG ARG TYR TRP MET ILE GLU GLU GLY ILE ILE ARG SEQRES 32 A 720 GLY ILE GLU PHE ALA ARG SER PRO ILE PRO THR GLU ASP SEQRES 33 A 720 GLU THR LYS ALA LEU GLN GLY ASN ASP ALA SER ALA ARG SEQRES 34 A 720 LYS GLU ALA ILE ASP LYS ILE ARG THR ARG TYR SER LYS SEQRES 35 A 720 PHE ALA ASN LYS ASP TYR SER ALA GLU VAL ASP LYS LYS SEQRES 36 A 720 VAL ALA VAL ALA MET LEU THR GLU TYR LEU LYS GLU ILE SEQRES 37 A 720 PRO TYR GLU ASN LEU PRO LEU HIS LEU ARG LEU VAL LYS SEQRES 38 A 720 ASP ARG PHE ALA GLY ASP VAL GLN ALA TYR VAL ASP ASP SEQRES 39 A 720 ILE PHE ALA ARG SER VAL PHE GLY SER GLU ALA GLN PHE SEQRES 40 A 720 ASP ALA PHE ALA ALA VAL PRO SER VAL GLU LYS LEU ALA SEQRES 41 A 720 GLU ASP PRO MET VAL LEU PHE ALA SER SER VAL PHE ASP SEQRES 42 A 720 GLU TYR ARG LYS LEU TYR ASN GLU LEU ARG PRO TYR ASP SEQRES 43 A 720 ASP PRO ILE LEU ARG ALA GLN ARG THR TYR ILE ALA GLY SEQRES 44 A 720 LEU LEU GLU MET ASP GLY ASP GLN ASP GLN PHE PRO ASP SEQRES 45 A 720 ALA ASN LEU THR LEU ARG PHE THR TYR GLY GLN VAL LYS SEQRES 46 A 720 GLY TYR SER PRO ARG ASP ASN VAL TYR TYR GLY HIS GLN SEQRES 47 A 720 THR THR LEU ASP GLY VAL MET GLU LYS GLU ASP PRO ASP SEQRES 48 A 720 ASN TRP GLU PHE VAL VAL ASP PRO LYS LEU LYS ALA VAL SEQRES 49 A 720 TYR GLU ARG LYS ASP PHE GLY ARG TYR ALA ASP ARG SER SEQRES 50 A 720 GLY ARG MET PRO VAL ALA PHE CYS ALA THR THR HIS THR SEQRES 51 A 720 THR GLY GLY ASN SER GLY SER PRO VAL MET ASN ALA ASN SEQRES 52 A 720 GLY GLU LEU ILE GLY LEU ASN PHE ASP ARG ASN TRP GLU SEQRES 53 A 720 GLY VAL GLY GLY ASP ILE GLN TYR LEU ALA ASP TYR GLN SEQRES 54 A 720 ARG SER ILE ILE VAL ASP ILE ARG TYR VAL LEU LEU VAL SEQRES 55 A 720 ILE ASP LYS VAL GLY GLY CYS GLN ARG LEU LEU ASP GLU SEQRES 56 A 720 MET ASN ILE VAL PRO HET K A 801 1 HET K A 802 1 HET GOL A 803 6 HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 K 2(K 1+) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *696(H2 O) HELIX 1 AA1 LEU A 27 GLN A 29 5 3 HELIX 2 AA2 GLN A 30 ARG A 41 1 12 HELIX 3 AA3 LYS A 46 TYR A 51 1 6 HELIX 4 AA4 SER A 57 ASP A 60 5 4 HELIX 5 AA5 ASN A 83 SER A 95 1 13 HELIX 6 AA6 ASN A 100 GLY A 105 1 6 HELIX 7 AA7 ARG A 110 GLU A 114 5 5 HELIX 8 AA8 VAL A 131 LYS A 140 1 10 HELIX 9 AA9 MET A 148 LEU A 151 5 4 HELIX 10 AB1 SER A 152 GLY A 165 1 14 HELIX 11 AB2 PRO A 206 LYS A 211 1 6 HELIX 12 AB3 THR A 284 ILE A 294 1 11 HELIX 13 AB4 ILE A 294 ASP A 317 1 24 HELIX 14 AB5 ASP A 317 ARG A 348 1 32 HELIX 15 AB6 GLY A 349 GLY A 369 1 21 HELIX 16 AB7 PRO A 371 ILE A 401 1 31 HELIX 17 AB8 ILE A 405 SER A 410 5 6 HELIX 18 AB9 LYS A 430 ALA A 444 1 15 HELIX 19 AC1 SER A 449 ILE A 468 1 20 HELIX 20 AC2 PRO A 469 LEU A 473 5 5 HELIX 21 AC3 PRO A 474 LEU A 477 5 4 HELIX 22 AC4 ARG A 478 ARG A 483 1 6 HELIX 23 AC5 ASP A 487 SER A 499 1 13 HELIX 24 AC6 SER A 503 ALA A 511 1 9 HELIX 25 AC7 ASP A 522 ARG A 543 1 22 HELIX 26 AC8 TYR A 545 GLY A 565 1 21 HELIX 27 AC9 LEU A 601 GLU A 608 1 8 HELIX 28 AD1 ASN A 612 VAL A 616 5 5 HELIX 29 AD2 ASP A 618 LYS A 628 1 11 HELIX 30 AD3 TRP A 675 ILE A 682 5 8 HELIX 31 AD4 ILE A 696 VAL A 706 1 11 HELIX 32 AD5 CYS A 709 MET A 716 1 8 SHEET 1 AA1 9 PHE A 106 TRP A 107 0 SHEET 2 AA1 9 ASP A 198 ALA A 204 -1 O ALA A 204 N PHE A 106 SHEET 3 AA1 9 SER A 229 ALA A 235 -1 O ILE A 230 N GLY A 203 SHEET 4 AA1 9 LEU A 79 THR A 82 -1 N VAL A 80 O PHE A 231 SHEET 5 AA1 9 CYS A 69 VAL A 73 -1 N GLU A 72 O LEU A 81 SHEET 6 AA1 9 VAL A 62 PHE A 65 -1 N PHE A 65 O CYS A 69 SHEET 7 AA1 9 VAL A 122 ASP A 130 -1 O VAL A 123 N LEU A 64 SHEET 8 AA1 9 LEU A 187 TYR A 196 -1 O MET A 190 N GLU A 129 SHEET 9 AA1 9 LEU A 175 PHE A 182 -1 N GLU A 178 O PHE A 191 SHEET 1 AA2 4 PHE A 106 TRP A 107 0 SHEET 2 AA2 4 ASP A 198 ALA A 204 -1 O ALA A 204 N PHE A 106 SHEET 3 AA2 4 SER A 229 ALA A 235 -1 O ILE A 230 N GLY A 203 SHEET 4 AA2 4 VAL A 249 PRO A 250 -1 O VAL A 249 N ALA A 235 SHEET 1 AA3 2 ILE A 259 SER A 260 0 SHEET 2 AA3 2 ILE A 718 VAL A 719 1 O VAL A 719 N ILE A 259 SHEET 1 AA4 7 ARG A 578 GLN A 583 0 SHEET 2 AA4 7 TYR A 269 GLY A 274 -1 N ILE A 272 O THR A 580 SHEET 3 AA4 7 PRO A 658 MET A 660 -1 O MET A 660 N MET A 271 SHEET 4 AA4 7 LEU A 666 ARG A 673 -1 O ILE A 667 N VAL A 659 SHEET 5 AA4 7 SER A 691 ASP A 695 -1 O VAL A 694 N LEU A 669 SHEET 6 AA4 7 PRO A 641 ALA A 646 -1 N ALA A 646 O SER A 691 SHEET 7 AA4 7 GLN A 598 THR A 600 -1 N THR A 599 O ALA A 643 SHEET 1 AA5 2 TYR A 587 ARG A 590 0 SHEET 2 AA5 2 VAL A 593 TYR A 595 -1 O TYR A 595 N TYR A 587 SSBOND 1 CYS A 69 CYS A 86 1555 1555 2.16 LINK OD1 ASN A 218 K K A 801 1555 1555 2.77 LINK O THR A 278 K K A 802 1555 1555 2.66 LINK OG1 THR A 278 K K A 802 1555 1555 3.12 LINK OG1 THR A 651 K K A 802 1555 1555 2.74 LINK OD1 ASP A 672 K K A 801 1555 1555 2.57 LINK OD2 ASP A 672 K K A 801 1555 1555 3.29 LINK OD2 ASP A 681 K K A 802 1555 1555 2.76 LINK K K A 801 O HOH A1583 1555 1555 3.30 LINK K K A 801 O HOH A1587 1555 1555 2.55 LINK K K A 802 O HOH A1059 1555 1555 2.76 LINK K K A 802 O HOH A1429 1555 1555 3.07 CISPEP 1 TRP A 221 PRO A 222 0 5.74 CISPEP 2 THR A 414 GLU A 415 0 16.12 CISPEP 3 ALA A 511 ALA A 512 0 -14.28 SITE 1 AC1 4 ASN A 218 TRP A 219 ASP A 672 HOH A1587 SITE 1 AC2 5 THR A 278 THR A 651 ASP A 681 HOH A1059 SITE 2 AC2 5 HOH A1429 SITE 1 AC3 8 ASP A 60 PHE A 124 LYS A 194 PRO A 253 SITE 2 AC3 8 LYS A 254 ARG A 255 HOH A 965 HOH A1432 CRYST1 99.140 103.280 175.310 90.00 90.00 90.00 C 2 2 21 8 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 0.010087 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005704 0.00000