PDB Short entry for 5FQU HEADER TRANSPORT PROTEIN 14-DEC-15 5FQU TITLE ORTHORHOMBIC CRYSTAL STRUCTURE OF OF PLPD (SELENOMETHIONINE TITLE 2 DERIVATIVE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PATATIN-LIKE PROTEIN, PLPD; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PASSENGER DOMAIN, UNP RESIDUES 20-333; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS TRANSPORT PROTEIN, BACTERIAL SECRETION, PHOSPHOLIPASE, LIPID KEYWDS 2 AFFINITY, INFECTION EXPDTA X-RAY DIFFRACTION AUTHOR P.VINICIUS DA MATA MADEIRA,S.ZOUHIR,P.BASSO,D.NEVES,A.LAUBIER, AUTHOR 2 R.SALACHA,S.BLEVES,E.FAUDRY,C.CONTRERAS-MARTEL,A.DESSEN REVDAT 3 27-SEP-17 5FQU 1 REMARK REVDAT 2 11-MAY-16 5FQU 1 JRNL REVDAT 1 06-APR-16 5FQU 0 JRNL AUTH P.V.DA MATA MADEIRA,S.ZOUHIR,P.BASSO,D.NEVES,A.LAUBIER, JRNL AUTH 2 R.SALACHA,S.BLEVES,E.FAUDRY,C.CONTRERAS-MARTEL,A.DESSEN JRNL TITL STRUCTURAL BASIS OF LIPID TARGETING AND DESTRUCTION BY THE JRNL TITL 2 TYPE V SECRETION SYSTEM OF PSEUDOMONAS AERUGINOSA. JRNL REF J.MOL.BIOL. V. 428 1790 2016 JRNL REFN ISSN 0022-2836 JRNL PMID 27012424 JRNL DOI 10.1016/J.JMB.2016.03.012 REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 17914 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 968 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) : 2.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1209 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.4440 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.4590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.82000 REMARK 3 B22 (A**2) : 18.06000 REMARK 3 B33 (A**2) : -8.24000 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): 0.629 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.305 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.331 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.334 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3750 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3785 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5086 ; 1.416 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8669 ; 0.866 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 491 ; 6.941 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;38.121 ;24.028 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 594 ;13.910 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;20.308 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 620 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4217 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 769 ; 0.004 ; 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): 1982 ; 6.596 ; 6.558 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1981 ; 6.576 ; 6.557 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2467 ; 9.451 ; 9.823 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1768 ; 8.194 ; 7.353 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 5FQU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1290065732. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97939 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19015 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740 REMARK 200 RESOLUTION RANGE LOW (A) : 85.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.01000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.810 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20%W/V PEG3350, 200MM SODIUM NITRATE, REMARK 280 0.6% N-DODECYL-BETA-D MALTOSIDE 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 23.37150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.20800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.69650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.20800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.37150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.69650 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: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLU A 20 REMARK 465 ALA A 21 REMARK 465 GLN A 89 REMARK 465 ALA A 90 REMARK 465 LEU A 91 REMARK 465 SER A 92 REMARK 465 ASP A 93 REMARK 465 ALA A 94 REMARK 465 PRO A 95 REMARK 465 PRO A 96 REMARK 465 ARG A 97 REMARK 465 LYS A 98 REMARK 465 ASP A 99 REMARK 465 VAL A 100 REMARK 465 PRO A 101 REMARK 465 PHE A 102 REMARK 465 ARG A 103 REMARK 465 ARG A 104 REMARK 465 LYS A 105 REMARK 465 GLN A 106 REMARK 465 ASP A 107 REMARK 465 ASP A 108 REMARK 465 ARG A 109 REMARK 465 ASP A 110 REMARK 465 PHE A 111 REMARK 465 LEU A 112 REMARK 465 VAL A 113 REMARK 465 LYS A 114 REMARK 465 GLN A 115 REMARK 465 LYS A 116 REMARK 465 ILE A 117 REMARK 465 SER A 118 REMARK 465 PHE A 119 REMARK 465 ARG A 120 REMARK 465 ASP A 121 REMARK 465 ASP A 122 REMARK 465 GLY A 123 REMARK 465 THR A 124 REMARK 465 LEU A 125 REMARK 465 GLY A 126 REMARK 465 LEU A 127 REMARK 465 ASP A 201 REMARK 465 GLY A 202 REMARK 465 ARG A 312 REMARK 465 LYS A 313 REMARK 465 PRO A 314 REMARK 465 LYS A 315 REMARK 465 ASP A 316 REMARK 465 LEU A 317 REMARK 465 ASN A 318 REMARK 465 SER A 319 REMARK 465 GLU A 320 REMARK 465 ALA A 321 REMARK 465 LEU A 322 REMARK 465 ASP A 323 REMARK 465 VAL A 324 REMARK 465 ALA A 325 REMARK 465 ARG A 326 REMARK 465 THR A 327 REMARK 465 PRO A 328 REMARK 465 ASN A 329 REMARK 465 GLN A 330 REMARK 465 ARG A 331 REMARK 465 LYS A 332 REMARK 465 PRO A 333 REMARK 465 GLU B 20 REMARK 465 ALA B 21 REMARK 465 GLN B 89 REMARK 465 ALA B 90 REMARK 465 LEU B 91 REMARK 465 SER B 92 REMARK 465 ASP B 93 REMARK 465 ALA B 94 REMARK 465 PRO B 95 REMARK 465 PRO B 96 REMARK 465 ARG B 97 REMARK 465 LYS B 98 REMARK 465 ASP B 99 REMARK 465 VAL B 100 REMARK 465 PRO B 101 REMARK 465 PHE B 102 REMARK 465 ARG B 103 REMARK 465 ARG B 104 REMARK 465 LYS B 105 REMARK 465 GLN B 106 REMARK 465 ASP B 107 REMARK 465 ASP B 108 REMARK 465 ARG B 109 REMARK 465 ASP B 110 REMARK 465 PHE B 111 REMARK 465 LEU B 112 REMARK 465 VAL B 113 REMARK 465 LYS B 114 REMARK 465 GLN B 115 REMARK 465 LYS B 116 REMARK 465 ILE B 117 REMARK 465 SER B 118 REMARK 465 PHE B 119 REMARK 465 ARG B 120 REMARK 465 ASP B 121 REMARK 465 ASP B 122 REMARK 465 GLY B 123 REMARK 465 THR B 124 REMARK 465 LEU B 125 REMARK 465 GLY B 126 REMARK 465 LEU B 127 REMARK 465 PRO B 128 REMARK 465 ASP B 201 REMARK 465 GLY B 202 REMARK 465 ARG B 312 REMARK 465 LYS B 313 REMARK 465 PRO B 314 REMARK 465 LYS B 315 REMARK 465 ASP B 316 REMARK 465 LEU B 317 REMARK 465 ASN B 318 REMARK 465 SER B 319 REMARK 465 GLU B 320 REMARK 465 ALA B 321 REMARK 465 LEU B 322 REMARK 465 ASP B 323 REMARK 465 VAL B 324 REMARK 465 ALA B 325 REMARK 465 ARG B 326 REMARK 465 THR B 327 REMARK 465 PRO B 328 REMARK 465 ASN B 329 REMARK 465 GLN B 330 REMARK 465 ARG B 331 REMARK 465 LYS B 332 REMARK 465 PRO B 333 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO A 128 CG CD REMARK 470 LEU A 129 CG CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 128 N - CA - CB ANGL. DEV. = 8.5 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 ALA A 33 -105.13 -130.70 REMARK 500 SER A 60 -111.49 30.70 REMARK 500 ARG A 152 -42.79 -133.15 REMARK 500 VAL A 194 -47.67 -134.96 REMARK 500 ASP A 207 128.87 -24.76 REMARK 500 PRO A 278 97.24 -69.37 REMARK 500 GLU A 310 49.46 -82.79 REMARK 500 ALA B 33 -105.47 -131.51 REMARK 500 SER B 60 -110.03 29.22 REMARK 500 ARG B 152 -41.33 -133.91 REMARK 500 VAL B 194 -46.46 -135.33 REMARK 500 ASP B 207 128.98 -26.60 REMARK 500 PRO B 278 96.30 -69.59 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 GLY A 281 TYR A 282 -137.57 REMARK 500 GLY B 281 TYR B 282 -137.93 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 AZI B 1312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1313 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1314 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SELENOMETHIONINE DERIVATIVE DBREF 5FQU A 20 333 UNP Q9HYQ6 Q9HYQ6_PSEAE 20 333 DBREF 5FQU B 20 333 UNP Q9HYQ6 Q9HYQ6_PSEAE 20 333 SEQRES 1 A 314 GLU ALA ARG PRO LYS ILE GLY LEU VAL LEU SER GLY GLY SEQRES 2 A 314 ALA ALA ARG GLY LEU ALA HIS ILE GLY VAL LEU LYS ALA SEQRES 3 A 314 LEU ASP GLU GLN GLY ILE GLN ILE ASP ALA ILE ALA GLY SEQRES 4 A 314 THR SER MSE GLY ALA VAL VAL GLY GLY LEU TYR ALA SER SEQRES 5 A 314 GLY TYR THR PRO ALA GLU LEU GLU ARG ILE ALA LEU GLU SEQRES 6 A 314 MSE ASP TRP GLN GLN ALA LEU SER ASP ALA PRO PRO ARG SEQRES 7 A 314 LYS ASP VAL PRO PHE ARG ARG LYS GLN ASP ASP ARG ASP SEQRES 8 A 314 PHE LEU VAL LYS GLN LYS ILE SER PHE ARG ASP ASP GLY SEQRES 9 A 314 THR LEU GLY LEU PRO LEU GLY VAL ILE GLN GLY GLN ASN SEQRES 10 A 314 LEU ALA MSE VAL LEU GLU SER LEU LEU VAL HIS THR SER SEQRES 11 A 314 ASP ASN ARG ASP PHE ASP LYS LEU ALA ILE PRO PHE ARG SEQRES 12 A 314 ALA VAL SER THR ASP ILE ALA THR GLY GLU LYS VAL VAL SEQRES 13 A 314 PHE ARG LYS GLY HIS LEU PRO GLN ALA ILE ARG ALA SER SEQRES 14 A 314 MSE SER ILE PRO ALA VAL PHE ALA PRO VAL GLU ILE ASP SEQRES 15 A 314 GLY ARG LEU LEU VAL ASP GLY GLY MSE VAL ASP ASN ILE SEQRES 16 A 314 PRO VAL ASP VAL ALA ARG ASP MSE GLY VAL ASP VAL VAL SEQRES 17 A 314 ILE VAL VAL ASP ILE GLY ASN PRO LEU ARG ASP ARG LYS SEQRES 18 A 314 ASP LEU SER THR VAL LEU ASP VAL MSE ASN GLN SER ILE SEQRES 19 A 314 THR LEU MSE THR ARG LYS ASN SER GLU ALA GLN LEU ALA SEQRES 20 A 314 THR LEU LYS PRO GLY ASP VAL LEU ILE GLN PRO PRO LEU SEQRES 21 A 314 SER GLY TYR GLY THR THR ASP PHE GLY ARG VAL PRO GLN SEQRES 22 A 314 LEU ILE ASP ALA GLY TYR ARG ALA THR THR VAL LEU ALA SEQRES 23 A 314 ALA ARG LEU ALA GLU LEU ARG LYS PRO LYS ASP LEU ASN SEQRES 24 A 314 SER GLU ALA LEU ASP VAL ALA ARG THR PRO ASN GLN ARG SEQRES 25 A 314 LYS PRO SEQRES 1 B 314 GLU ALA ARG PRO LYS ILE GLY LEU VAL LEU SER GLY GLY SEQRES 2 B 314 ALA ALA ARG GLY LEU ALA HIS ILE GLY VAL LEU LYS ALA SEQRES 3 B 314 LEU ASP GLU GLN GLY ILE GLN ILE ASP ALA ILE ALA GLY SEQRES 4 B 314 THR SER MSE GLY ALA VAL VAL GLY GLY LEU TYR ALA SER SEQRES 5 B 314 GLY TYR THR PRO ALA GLU LEU GLU ARG ILE ALA LEU GLU SEQRES 6 B 314 MSE ASP TRP GLN GLN ALA LEU SER ASP ALA PRO PRO ARG SEQRES 7 B 314 LYS ASP VAL PRO PHE ARG ARG LYS GLN ASP ASP ARG ASP SEQRES 8 B 314 PHE LEU VAL LYS GLN LYS ILE SER PHE ARG ASP ASP GLY SEQRES 9 B 314 THR LEU GLY LEU PRO LEU GLY VAL ILE GLN GLY GLN ASN SEQRES 10 B 314 LEU ALA MSE VAL LEU GLU SER LEU LEU VAL HIS THR SER SEQRES 11 B 314 ASP ASN ARG ASP PHE ASP LYS LEU ALA ILE PRO PHE ARG SEQRES 12 B 314 ALA VAL SER THR ASP ILE ALA THR GLY GLU LYS VAL VAL SEQRES 13 B 314 PHE ARG LYS GLY HIS LEU PRO GLN ALA ILE ARG ALA SER SEQRES 14 B 314 MSE SER ILE PRO ALA VAL PHE ALA PRO VAL GLU ILE ASP SEQRES 15 B 314 GLY ARG LEU LEU VAL ASP GLY GLY MSE VAL ASP ASN ILE SEQRES 16 B 314 PRO VAL ASP VAL ALA ARG ASP MSE GLY VAL ASP VAL VAL SEQRES 17 B 314 ILE VAL VAL ASP ILE GLY ASN PRO LEU ARG ASP ARG LYS SEQRES 18 B 314 ASP LEU SER THR VAL LEU ASP VAL MSE ASN GLN SER ILE SEQRES 19 B 314 THR LEU MSE THR ARG LYS ASN SER GLU ALA GLN LEU ALA SEQRES 20 B 314 THR LEU LYS PRO GLY ASP VAL LEU ILE GLN PRO PRO LEU SEQRES 21 B 314 SER GLY TYR GLY THR THR ASP PHE GLY ARG VAL PRO GLN SEQRES 22 B 314 LEU ILE ASP ALA GLY TYR ARG ALA THR THR VAL LEU ALA SEQRES 23 B 314 ALA ARG LEU ALA GLU LEU ARG LYS PRO LYS ASP LEU ASN SEQRES 24 B 314 SER GLU ALA LEU ASP VAL ALA ARG THR PRO ASN GLN ARG SEQRES 25 B 314 LYS PRO MODRES 5FQU MSE A 61 MET SELENOMETHIONINE MODRES 5FQU MSE A 85 MET SELENOMETHIONINE MODRES 5FQU MSE A 139 MET SELENOMETHIONINE MODRES 5FQU MSE A 189 MET SELENOMETHIONINE MODRES 5FQU MSE A 210 MET SELENOMETHIONINE MODRES 5FQU MSE A 222 MET SELENOMETHIONINE MODRES 5FQU MSE A 249 MET SELENOMETHIONINE MODRES 5FQU MSE A 256 MET SELENOMETHIONINE MODRES 5FQU MSE B 61 MET SELENOMETHIONINE MODRES 5FQU MSE B 85 MET SELENOMETHIONINE MODRES 5FQU MSE B 139 MET SELENOMETHIONINE MODRES 5FQU MSE B 189 MET SELENOMETHIONINE MODRES 5FQU MSE B 210 MET SELENOMETHIONINE MODRES 5FQU MSE B 222 MET SELENOMETHIONINE MODRES 5FQU MSE B 249 MET SELENOMETHIONINE MODRES 5FQU MSE B 256 MET SELENOMETHIONINE HET MSE A 61 8 HET MSE A 85 8 HET MSE A 139 8 HET MSE A 189 8 HET MSE A 210 8 HET MSE A 222 8 HET MSE A 249 8 HET MSE A 256 8 HET MSE B 61 8 HET MSE B 85 8 HET MSE B 139 8 HET MSE B 189 8 HET MSE B 210 8 HET MSE B 222 8 HET MSE B 249 8 HET MSE B 256 8 HET AZI B1312 3 HET NA B1313 1 HET NA B1314 1 HETNAM MSE SELENOMETHIONINE HETNAM AZI AZIDE ION HETNAM NA SODIUM ION FORMUL 1 MSE 16(C5 H11 N O2 SE) FORMUL 3 AZI N3 1- FORMUL 4 NA 2(NA 1+) FORMUL 6 HOH *61(H2 O) HELIX 1 1 ALA A 33 GLY A 36 5 4 HELIX 2 2 LEU A 37 GLN A 49 1 13 HELIX 3 3 SER A 60 GLY A 72 1 13 HELIX 4 4 THR A 74 GLU A 84 1 11 HELIX 5 5 LEU A 129 LEU A 145 1 17 HELIX 6 6 VAL A 146 SER A 149 5 4 HELIX 7 7 PHE A 154 LEU A 157 5 4 HELIX 8 8 HIS A 180 MSE A 189 1 10 HELIX 9 9 GLY A 208 ASN A 213 1 6 HELIX 10 10 PRO A 215 ASP A 221 1 7 HELIX 11 11 ASP A 238 LEU A 242 5 5 HELIX 12 12 THR A 244 THR A 267 1 24 HELIX 13 13 ARG A 289 VAL A 303 1 15 HELIX 14 14 LEU A 304 GLU A 310 1 7 HELIX 15 15 ALA B 33 GLY B 36 5 4 HELIX 16 16 LEU B 37 GLN B 49 1 13 HELIX 17 17 SER B 60 GLY B 72 1 13 HELIX 18 18 THR B 74 GLU B 84 1 11 HELIX 19 19 LEU B 129 LEU B 145 1 17 HELIX 20 20 VAL B 146 SER B 149 5 4 HELIX 21 21 PHE B 154 LEU B 157 5 4 HELIX 22 22 HIS B 180 MSE B 189 1 10 HELIX 23 23 GLY B 208 ASN B 213 1 6 HELIX 24 24 PRO B 215 ASP B 221 1 7 HELIX 25 25 ASP B 238 LEU B 242 5 5 HELIX 26 26 THR B 244 THR B 267 1 24 HELIX 27 27 ARG B 289 VAL B 303 1 15 HELIX 28 28 LEU B 304 GLU B 310 1 7 SHEET 1 AA 2 LYS A 173 PHE A 176 0 SHEET 2 AA 2 PHE A 161 ASP A 167 -1 O ALA A 163 N PHE A 176 SHEET 1 AB 4 VAL A 198 GLU A 199 0 SHEET 2 AB 4 LEU A 204 ASP A 207 1 O LEU A 205 N VAL A 198 SHEET 3 AB 4 PHE A 161 ASP A 167 -1 O THR A 166 N VAL A 206 SHEET 4 AB 4 LYS A 173 PHE A 176 -1 O VAL A 174 N SER A 165 SHEET 1 AC 7 VAL A 198 GLU A 199 0 SHEET 2 AC 7 LEU A 204 ASP A 207 1 O LEU A 205 N VAL A 198 SHEET 3 AC 7 PHE A 161 ASP A 167 -1 O THR A 166 N VAL A 206 SHEET 4 AC 7 ALA A 55 THR A 59 1 O ILE A 56 N ARG A 162 SHEET 5 AC 7 ILE A 25 LEU A 29 1 O LEU A 27 N ALA A 57 SHEET 6 AC 7 VAL A 226 VAL A 230 1 O VAL A 226 N GLY A 26 SHEET 7 AC 7 VAL A 273 ILE A 275 1 O VAL A 273 N VAL A 229 SHEET 1 BA 2 LYS B 173 PHE B 176 0 SHEET 2 BA 2 PHE B 161 ASP B 167 -1 O ALA B 163 N PHE B 176 SHEET 1 BB 4 VAL B 198 GLU B 199 0 SHEET 2 BB 4 LEU B 204 ASP B 207 1 O LEU B 205 N VAL B 198 SHEET 3 BB 4 PHE B 161 ASP B 167 -1 O THR B 166 N VAL B 206 SHEET 4 BB 4 LYS B 173 PHE B 176 -1 O VAL B 174 N SER B 165 SHEET 1 BC 7 VAL B 198 GLU B 199 0 SHEET 2 BC 7 LEU B 204 ASP B 207 1 O LEU B 205 N VAL B 198 SHEET 3 BC 7 PHE B 161 ASP B 167 -1 O THR B 166 N VAL B 206 SHEET 4 BC 7 ALA B 55 THR B 59 1 O ILE B 56 N ARG B 162 SHEET 5 BC 7 ILE B 25 LEU B 29 1 O LEU B 27 N ALA B 57 SHEET 6 BC 7 VAL B 226 VAL B 230 1 O VAL B 226 N GLY B 26 SHEET 7 BC 7 VAL B 273 ILE B 275 1 O VAL B 273 N VAL B 229 LINK C SER A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N GLY A 62 1555 1555 1.33 LINK C GLU A 84 N MSE A 85 1555 1555 1.33 LINK C MSE A 85 N ASP A 86 1555 1555 1.34 LINK C ALA A 138 N MSE A 139 1555 1555 1.32 LINK C MSE A 139 N VAL A 140 1555 1555 1.33 LINK C SER A 188 N MSE A 189 1555 1555 1.32 LINK C MSE A 189 N SER A 190 1555 1555 1.33 LINK C GLY A 209 N MSE A 210 1555 1555 1.33 LINK C MSE A 210 N VAL A 211 1555 1555 1.33 LINK C ASP A 221 N MSE A 222 1555 1555 1.33 LINK C MSE A 222 N GLY A 223 1555 1555 1.33 LINK C VAL A 248 N MSE A 249 1555 1555 1.33 LINK C MSE A 249 N ASN A 250 1555 1555 1.33 LINK C LEU A 255 N MSE A 256 1555 1555 1.34 LINK C MSE A 256 N THR A 257 1555 1555 1.33 LINK C SER B 60 N MSE B 61 1555 1555 1.33 LINK C MSE B 61 N GLY B 62 1555 1555 1.33 LINK C GLU B 84 N MSE B 85 1555 1555 1.34 LINK C MSE B 85 N ASP B 86 1555 1555 1.34 LINK C ALA B 138 N MSE B 139 1555 1555 1.33 LINK C MSE B 139 N VAL B 140 1555 1555 1.32 LINK C SER B 188 N MSE B 189 1555 1555 1.32 LINK C MSE B 189 N SER B 190 1555 1555 1.33 LINK C GLY B 209 N MSE B 210 1555 1555 1.33 LINK C MSE B 210 N VAL B 211 1555 1555 1.33 LINK C ASP B 221 N MSE B 222 1555 1555 1.33 LINK C MSE B 222 N GLY B 223 1555 1555 1.33 LINK C VAL B 248 N MSE B 249 1555 1555 1.33 LINK C MSE B 249 N ASN B 250 1555 1555 1.33 LINK C LEU B 255 N MSE B 256 1555 1555 1.34 LINK C MSE B 256 N THR B 257 1555 1555 1.33 LINK N3 AZI B1312 NA NA B1314 1555 1555 2.92 LINK N1 AZI B1312 NA NA B1313 1555 1555 2.97 SITE 1 AC1 5 GLU A 199 ILE A 200 ILE B 200 NA B1313 SITE 2 AC1 5 NA B1314 SITE 1 AC2 2 ARG B 239 AZI B1312 SITE 1 AC3 2 ARG B 203 AZI B1312 CRYST1 46.743 113.393 130.416 90.00 90.00 90.00 P 21 21 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 0.021394 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008819 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007668 0.00000