HEADER LIGASE 16-JUN-14 4TRH TITLE THE LEGIONELLA EFFECTOR SIDC DEFINES A UNIQUE FAMILY OF UBIQUITIN TITLE 2 LIGASES IMPORTANT FOR BACTERIAL PHAGOSOMAL REMODELING COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIDC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-542; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 446; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS SIDC, SNL, UBIQUITIN, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR F.S.HSU,X.LUO,J.QIU,Y.TENG,J.JIN,M.B.SMOLKA,Z.Q.LUO,Y.MAO REVDAT 7 27-DEC-23 4TRH 1 REMARK REVDAT 6 25-DEC-19 4TRH 1 REMARK REVDAT 5 13-SEP-17 4TRH 1 REMARK REVDAT 4 07-OCT-15 4TRH 1 REMARK REVDAT 3 01-OCT-14 4TRH 1 JRNL REVDAT 2 23-JUL-14 4TRH 1 JRNL REVDAT 1 02-JUL-14 4TRH 0 JRNL AUTH F.HSU,X.LUO,J.QIU,Y.B.TENG,J.JIN,M.B.SMOLKA,Z.Q.LUO,Y.MAO JRNL TITL THE LEGIONELLA EFFECTOR SIDC DEFINES A UNIQUE FAMILY OF JRNL TITL 2 UBIQUITIN LIGASES IMPORTANT FOR BACTERIAL PHAGOSOMAL JRNL TITL 3 REMODELING. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 10538 2014 JRNL REFN ESSN 1091-6490 JRNL PMID 25006264 JRNL DOI 10.1073/PNAS.1402605111 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 85289 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4493 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) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5805 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2930 REMARK 3 BIN FREE R VALUE SET COUNT : 310 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8236 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.14000 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): 0.180 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.806 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8435 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7996 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11392 ; 1.765 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18532 ; 1.208 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1023 ; 5.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 432 ;33.726 ;25.324 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1565 ;16.325 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.627 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1234 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9553 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1875 ; 0.005 ; 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): 4080 ; 3.810 ; 4.002 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4079 ; 3.791 ; 4.001 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5101 ; 5.425 ; 5.980 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 5102 ; 5.427 ; 5.982 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4355 ; 4.498 ; 4.434 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4356 ; 4.498 ; 4.435 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 6290 ; 6.912 ; 6.468 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9694 ; 9.029 ;31.461 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9632 ; 9.037 ;31.431 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 8 514 B 8 514 30544 0.11 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 516 REMARK 3 ORIGIN FOR THE GROUP (A): 30.2914 59.4843 9.8704 REMARK 3 T TENSOR REMARK 3 T11: 0.1201 T22: 0.0504 REMARK 3 T33: 0.0725 T12: 0.0004 REMARK 3 T13: 0.0056 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 0.3321 L22: 0.0734 REMARK 3 L33: 0.1996 L12: -0.1024 REMARK 3 L13: 0.1044 L23: 0.0037 REMARK 3 S TENSOR REMARK 3 S11: -0.0263 S12: 0.0126 S13: 0.0871 REMARK 3 S21: 0.0244 S22: 0.0350 S23: -0.0151 REMARK 3 S31: -0.0865 S32: 0.0358 S33: -0.0087 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 515 REMARK 3 ORIGIN FOR THE GROUP (A): 17.2222 67.2980 34.5527 REMARK 3 T TENSOR REMARK 3 T11: 0.1738 T22: 0.0816 REMARK 3 T33: 0.1880 T12: 0.0545 REMARK 3 T13: 0.1516 T23: 0.0626 REMARK 3 L TENSOR REMARK 3 L11: 0.1945 L22: 0.5347 REMARK 3 L33: 0.2828 L12: 0.0478 REMARK 3 L13: 0.0878 L23: 0.2056 REMARK 3 S TENSOR REMARK 3 S11: -0.0979 S12: 0.0143 S13: -0.0277 REMARK 3 S21: 0.1380 S22: 0.2049 S23: 0.1607 REMARK 3 S31: -0.0731 S32: 0.0793 S33: -0.1070 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 4TRH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90100 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 35.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CACODYLATE PH 5.6, 7.5% PEG6000, REMARK 280 AND 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 30.61500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.68450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.34250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.68450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.61500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.34250 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: 4690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 MET A 1 REMARK 465 VAL A 2 REMARK 465 ILE A 3 REMARK 465 ASN A 4 REMARK 465 MET A 5 REMARK 465 VAL A 6 REMARK 465 ASP A 7 REMARK 465 ASP A 517 REMARK 465 GLN A 518 REMARK 465 PHE A 519 REMARK 465 LYS A 520 REMARK 465 LYS A 521 REMARK 465 GLU A 522 REMARK 465 VAL A 523 REMARK 465 VAL A 524 REMARK 465 LYS A 525 REMARK 465 LEU A 526 REMARK 465 LEU A 527 REMARK 465 ALA A 528 REMARK 465 GLU A 529 REMARK 465 ASN A 530 REMARK 465 LYS A 531 REMARK 465 PRO A 532 REMARK 465 LYS A 533 REMARK 465 GLU A 534 REMARK 465 LEU A 535 REMARK 465 LEU A 536 REMARK 465 ASP A 537 REMARK 465 TYR A 538 REMARK 465 LEU A 539 REMARK 465 VAL A 540 REMARK 465 ALA A 541 REMARK 465 THR A 542 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 ILE B 3 REMARK 465 ASN B 4 REMARK 465 MET B 5 REMARK 465 VAL B 6 REMARK 465 ASP B 7 REMARK 465 LEU B 516 REMARK 465 ASP B 517 REMARK 465 GLN B 518 REMARK 465 PHE B 519 REMARK 465 LYS B 520 REMARK 465 LYS B 521 REMARK 465 GLU B 522 REMARK 465 VAL B 523 REMARK 465 VAL B 524 REMARK 465 LYS B 525 REMARK 465 LEU B 526 REMARK 465 LEU B 527 REMARK 465 ALA B 528 REMARK 465 GLU B 529 REMARK 465 ASN B 530 REMARK 465 LYS B 531 REMARK 465 PRO B 532 REMARK 465 LYS B 533 REMARK 465 GLU B 534 REMARK 465 LEU B 535 REMARK 465 LEU B 536 REMARK 465 ASP B 537 REMARK 465 TYR B 538 REMARK 465 LEU B 539 REMARK 465 VAL B 540 REMARK 465 ALA B 541 REMARK 465 THR B 542 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 OD1 ASP A 301 OD1 ASP A 303 2.18 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 608 O HOH B 603 4555 2.06 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 GLU A 149 CD GLU A 149 OE1 0.071 REMARK 500 CYS A 468 CB CYS A 468 SG -0.127 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 31 CA - CB - CG ANGL. DEV. = -16.7 DEGREES REMARK 500 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 188 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 465 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 465 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 CYS A 468 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 LEU B 31 CA - CB - CG ANGL. DEV. = -18.1 DEGREES REMARK 500 ARG B 207 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 MET B 298 CG - SD - CE ANGL. DEV. = -10.7 DEGREES REMARK 500 ASP B 333 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 465 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 465 NE - CZ - NH2 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 TYR A 19 -1.29 78.20 REMARK 500 THR A 45 -127.53 39.94 REMARK 500 THR A 45 -127.15 39.94 REMARK 500 PRO A 95 -34.31 -32.27 REMARK 500 PHE A 170 51.07 -91.01 REMARK 500 ASN A 221 64.96 -109.11 REMARK 500 GLU A 514 8.67 -62.41 REMARK 500 TYR B 19 -2.38 75.39 REMARK 500 THR B 45 -130.32 49.92 REMARK 500 PRO B 95 -34.15 -35.11 REMARK 500 PHE B 170 49.33 -85.09 REMARK 500 ASN B 221 64.89 -105.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4TRG RELATED DB: PDB REMARK 900 NATIVE TYPE DBREF 4TRH A 1 542 UNP Q6RCR4 Q6RCR4_LEGPN 1 542 DBREF 4TRH B 1 542 UNP Q6RCR4 Q6RCR4_LEGPN 1 542 SEQRES 1 A 542 MET VAL ILE ASN MET VAL ASP VAL ILE LYS PHE LYS GLU SEQRES 2 A 542 PRO GLU ARG CYS ASP TYR LEU TYR VAL ASP GLU ASN ASN SEQRES 3 A 542 LYS VAL HIS ILE LEU LEU PRO ILE VAL GLY GLY ASP GLU SEQRES 4 A 542 ILE GLY LEU ASP ASN THR CYS GLN THR ALA VAL GLU LEU SEQRES 5 A 542 ILE THR PHE PHE TYR GLY SER ALA HIS SER GLY VAL THR SEQRES 6 A 542 LYS TYR SER ALA GLU HIS GLN LEU SER GLU TYR LYS ARG SEQRES 7 A 542 GLN LEU GLU GLU ASP ILE LYS ALA ILE ASN SER GLN LYS SEQRES 8 A 542 LYS ILE SER PRO HIS ALA TYR ASP ASP LEU LEU LYS GLU SEQRES 9 A 542 LYS ILE GLU ARG LEU GLN GLN ILE GLU LYS TYR ILE GLU SEQRES 10 A 542 LEU ILE GLN VAL LEU LYS LYS GLN TYR ASP GLU GLN ASN SEQRES 11 A 542 ASP ILE ARG GLN LEU ARG THR GLY GLY ILE PRO GLN LEU SEQRES 12 A 542 PRO SER GLY VAL LYS GLU ILE ILE LYS SER SER GLU ASN SEQRES 13 A 542 ALA PHE ALA VAL ARG LEU SER PRO TYR ASP ASN ASP LYS SEQRES 14 A 542 PHE THR ARG PHE ASP ASP PRO LEU PHE ASN VAL LYS ARG SEQRES 15 A 542 ASN ILE SER LYS TYR ASP THR PRO SER ARG GLN ALA PRO SEQRES 16 A 542 ILE PRO ILE TYR GLU GLY LEU GLY TYR ARG LEU ARG SER SEQRES 17 A 542 THR LEU PHE PRO GLU ASP LYS THR PRO THR PRO ILE ASN SEQRES 18 A 542 LYS LYS SER LEU ARG ASP LYS VAL LYS SER THR VAL LEU SEQRES 19 A 542 SER HIS TYR LYS ASP GLU ASP ARG ILE ASP GLY GLU LYS SEQRES 20 A 542 LYS ASP GLU LYS LEU ASN GLU LEU ILE THR ASN LEU GLN SEQRES 21 A 542 ASN GLU LEU VAL LYS GLU LEU VAL LYS SER ASP PRO GLN SEQRES 22 A 542 TYR SER LYS LEU SER LEU SER LYS ASP PRO ARG GLY LYS SEQRES 23 A 542 GLU ILE ASN TYR ASP TYR LEU VAL ASN SER LEU MET LEU SEQRES 24 A 542 VAL ASP ASN ASP SER GLU ILE GLY ASP TRP ILE ASP THR SEQRES 25 A 542 ILE LEU ASP ALA THR VAL ASP SER THR VAL TRP VAL ALA SEQRES 26 A 542 GLN ALA SER SER PRO PHE TYR ASP GLY ALA LYS GLU ILE SEQRES 27 A 542 SER SER ASP ARG ASP ALA ASP LYS ILE SER ILE ARG VAL SEQRES 28 A 542 GLN TYR LEU LEU ALA GLU ALA ASN ILE TYR CYS LYS THR SEQRES 29 A 542 ASN LYS LEU SER ASP ALA ASN PHE GLY GLU PHE PHE ASP SEQRES 30 A 542 LYS GLU PRO HIS ALA THR GLU ILE ALA LYS ARG VAL LYS SEQRES 31 A 542 GLU GLY PHE THR GLN GLY ALA ASP ILE GLU PRO ILE ILE SEQRES 32 A 542 TYR ASP TYR ILE ASN SER ASN HIS ALA GLU LEU GLY LEU SEQRES 33 A 542 LYS SER PRO LEU THR GLY LYS GLN GLN GLN GLU ILE THR SEQRES 34 A 542 ASP LYS PHE THR LYS HIS TYR ASN THR ILE LYS GLU SER SEQRES 35 A 542 PRO HIS PHE ASP GLU PHE PHE VAL ALA ASP PRO ASP LYS SEQRES 36 A 542 LYS GLY ASN ILE PHE SER HIS GLN GLY ARG ILE SER CYS SEQRES 37 A 542 HIS PHE LEU ASP PHE PHE THR ARG GLN THR LYS GLY LYS SEQRES 38 A 542 HIS PRO LEU GLY ASP LEU ALA SER HIS GLN GLU ALA LEU SEQRES 39 A 542 GLN GLU GLY THR SER ASN ARG LEU HIS HIS LYS ASN GLU SEQRES 40 A 542 VAL VAL ALA GLN GLY TYR GLU LYS LEU ASP GLN PHE LYS SEQRES 41 A 542 LYS GLU VAL VAL LYS LEU LEU ALA GLU ASN LYS PRO LYS SEQRES 42 A 542 GLU LEU LEU ASP TYR LEU VAL ALA THR SEQRES 1 B 542 MET VAL ILE ASN MET VAL ASP VAL ILE LYS PHE LYS GLU SEQRES 2 B 542 PRO GLU ARG CYS ASP TYR LEU TYR VAL ASP GLU ASN ASN SEQRES 3 B 542 LYS VAL HIS ILE LEU LEU PRO ILE VAL GLY GLY ASP GLU SEQRES 4 B 542 ILE GLY LEU ASP ASN THR CYS GLN THR ALA VAL GLU LEU SEQRES 5 B 542 ILE THR PHE PHE TYR GLY SER ALA HIS SER GLY VAL THR SEQRES 6 B 542 LYS TYR SER ALA GLU HIS GLN LEU SER GLU TYR LYS ARG SEQRES 7 B 542 GLN LEU GLU GLU ASP ILE LYS ALA ILE ASN SER GLN LYS SEQRES 8 B 542 LYS ILE SER PRO HIS ALA TYR ASP ASP LEU LEU LYS GLU SEQRES 9 B 542 LYS ILE GLU ARG LEU GLN GLN ILE GLU LYS TYR ILE GLU SEQRES 10 B 542 LEU ILE GLN VAL LEU LYS LYS GLN TYR ASP GLU GLN ASN SEQRES 11 B 542 ASP ILE ARG GLN LEU ARG THR GLY GLY ILE PRO GLN LEU SEQRES 12 B 542 PRO SER GLY VAL LYS GLU ILE ILE LYS SER SER GLU ASN SEQRES 13 B 542 ALA PHE ALA VAL ARG LEU SER PRO TYR ASP ASN ASP LYS SEQRES 14 B 542 PHE THR ARG PHE ASP ASP PRO LEU PHE ASN VAL LYS ARG SEQRES 15 B 542 ASN ILE SER LYS TYR ASP THR PRO SER ARG GLN ALA PRO SEQRES 16 B 542 ILE PRO ILE TYR GLU GLY LEU GLY TYR ARG LEU ARG SER SEQRES 17 B 542 THR LEU PHE PRO GLU ASP LYS THR PRO THR PRO ILE ASN SEQRES 18 B 542 LYS LYS SER LEU ARG ASP LYS VAL LYS SER THR VAL LEU SEQRES 19 B 542 SER HIS TYR LYS ASP GLU ASP ARG ILE ASP GLY GLU LYS SEQRES 20 B 542 LYS ASP GLU LYS LEU ASN GLU LEU ILE THR ASN LEU GLN SEQRES 21 B 542 ASN GLU LEU VAL LYS GLU LEU VAL LYS SER ASP PRO GLN SEQRES 22 B 542 TYR SER LYS LEU SER LEU SER LYS ASP PRO ARG GLY LYS SEQRES 23 B 542 GLU ILE ASN TYR ASP TYR LEU VAL ASN SER LEU MET LEU SEQRES 24 B 542 VAL ASP ASN ASP SER GLU ILE GLY ASP TRP ILE ASP THR SEQRES 25 B 542 ILE LEU ASP ALA THR VAL ASP SER THR VAL TRP VAL ALA SEQRES 26 B 542 GLN ALA SER SER PRO PHE TYR ASP GLY ALA LYS GLU ILE SEQRES 27 B 542 SER SER ASP ARG ASP ALA ASP LYS ILE SER ILE ARG VAL SEQRES 28 B 542 GLN TYR LEU LEU ALA GLU ALA ASN ILE TYR CYS LYS THR SEQRES 29 B 542 ASN LYS LEU SER ASP ALA ASN PHE GLY GLU PHE PHE ASP SEQRES 30 B 542 LYS GLU PRO HIS ALA THR GLU ILE ALA LYS ARG VAL LYS SEQRES 31 B 542 GLU GLY PHE THR GLN GLY ALA ASP ILE GLU PRO ILE ILE SEQRES 32 B 542 TYR ASP TYR ILE ASN SER ASN HIS ALA GLU LEU GLY LEU SEQRES 33 B 542 LYS SER PRO LEU THR GLY LYS GLN GLN GLN GLU ILE THR SEQRES 34 B 542 ASP LYS PHE THR LYS HIS TYR ASN THR ILE LYS GLU SER SEQRES 35 B 542 PRO HIS PHE ASP GLU PHE PHE VAL ALA ASP PRO ASP LYS SEQRES 36 B 542 LYS GLY ASN ILE PHE SER HIS GLN GLY ARG ILE SER CYS SEQRES 37 B 542 HIS PHE LEU ASP PHE PHE THR ARG GLN THR LYS GLY LYS SEQRES 38 B 542 HIS PRO LEU GLY ASP LEU ALA SER HIS GLN GLU ALA LEU SEQRES 39 B 542 GLN GLU GLY THR SER ASN ARG LEU HIS HIS LYS ASN GLU SEQRES 40 B 542 VAL VAL ALA GLN GLY TYR GLU LYS LEU ASP GLN PHE LYS SEQRES 41 B 542 LYS GLU VAL VAL LYS LEU LEU ALA GLU ASN LYS PRO LYS SEQRES 42 B 542 GLU LEU LEU ASP TYR LEU VAL ALA THR FORMUL 3 HOH *233(H2 O) HELIX 1 AA1 ASN A 44 THR A 48 5 5 HELIX 2 AA2 ALA A 49 GLY A 58 1 10 HELIX 3 AA3 SER A 68 GLN A 90 1 23 HELIX 4 AA4 TYR A 98 TYR A 126 1 29 HELIX 5 AA5 ARG A 133 GLY A 138 1 6 HELIX 6 AA6 PRO A 144 SER A 154 1 11 HELIX 7 AA7 SER A 185 THR A 189 5 5 HELIX 8 AA8 GLY A 201 PHE A 211 1 11 HELIX 9 AA9 SER A 224 SER A 235 1 12 HELIX 10 AB1 LYS A 247 LYS A 269 1 23 HELIX 11 AB2 ASP A 271 LEU A 277 5 7 HELIX 12 AB3 ASN A 289 ASN A 295 1 7 HELIX 13 AB4 GLU A 305 VAL A 318 1 14 HELIX 14 AB5 ASP A 319 VAL A 324 5 6 HELIX 15 AB6 SER A 340 ASN A 365 1 26 HELIX 16 AB7 ASN A 371 LYS A 378 1 8 HELIX 17 AB8 PRO A 380 GLN A 395 1 16 HELIX 18 AB9 ASP A 398 ASN A 410 1 13 HELIX 19 AC1 THR A 421 LYS A 440 1 20 HELIX 20 AC2 PHE A 470 THR A 478 1 9 HELIX 21 AC3 LEU A 484 ALA A 488 5 5 HELIX 22 AC4 SER A 489 GLU A 496 1 8 HELIX 23 AC5 ASN A 506 ALA A 510 5 5 HELIX 24 AC6 ASN B 44 THR B 48 5 5 HELIX 25 AC7 ALA B 49 GLY B 58 1 10 HELIX 26 AC8 SER B 68 LYS B 91 1 24 HELIX 27 AC9 TYR B 98 GLN B 125 1 28 HELIX 28 AD1 ARG B 133 GLY B 138 1 6 HELIX 29 AD2 PRO B 144 SER B 153 1 10 HELIX 30 AD3 SER B 185 THR B 189 5 5 HELIX 31 AD4 GLY B 201 PHE B 211 1 11 HELIX 32 AD5 SER B 224 SER B 235 1 12 HELIX 33 AD6 LYS B 247 LYS B 269 1 23 HELIX 34 AD7 ASP B 271 LEU B 277 5 7 HELIX 35 AD8 ASN B 289 ASN B 295 1 7 HELIX 36 AD9 GLU B 305 VAL B 318 1 14 HELIX 37 AE1 ASP B 319 VAL B 324 5 6 HELIX 38 AE2 SER B 340 ASN B 365 1 26 HELIX 39 AE3 ASN B 371 ASP B 377 1 7 HELIX 40 AE4 PRO B 380 GLN B 395 1 16 HELIX 41 AE5 ASP B 398 ASN B 410 1 13 HELIX 42 AE6 THR B 421 LYS B 440 1 20 HELIX 43 AE7 PHE B 470 LYS B 479 1 10 HELIX 44 AE8 LEU B 484 ALA B 488 5 5 HELIX 45 AE9 SER B 489 GLU B 496 1 8 HELIX 46 AF1 ASN B 506 GLN B 511 1 6 SHEET 1 AA1 5 LEU A 20 VAL A 22 0 SHEET 2 AA1 5 VAL A 28 GLY A 36 -1 O HIS A 29 N TYR A 21 SHEET 3 AA1 5 ARG A 465 HIS A 469 -1 O ILE A 466 N ILE A 34 SHEET 4 AA1 5 ILE A 459 HIS A 462 -1 N PHE A 460 O SER A 467 SHEET 5 AA1 5 ARG A 501 LEU A 502 1 O LEU A 502 N SER A 461 SHEET 1 AA2 2 SER A 59 HIS A 61 0 SHEET 2 AA2 2 VAL A 64 LYS A 66 -1 O LYS A 66 N SER A 59 SHEET 1 AA3 2 ALA A 157 ARG A 161 0 SHEET 2 AA3 2 GLU A 447 ALA A 451 -1 O VAL A 450 N PHE A 158 SHEET 1 AA4 2 THR A 218 PRO A 219 0 SHEET 2 AA4 2 GLU A 337 ILE A 338 -1 O ILE A 338 N THR A 218 SHEET 1 AA5 5 LEU B 20 VAL B 22 0 SHEET 2 AA5 5 VAL B 28 GLY B 36 -1 O HIS B 29 N TYR B 21 SHEET 3 AA5 5 ARG B 465 HIS B 469 -1 O ILE B 466 N VAL B 35 SHEET 4 AA5 5 ILE B 459 HIS B 462 -1 N PHE B 460 O SER B 467 SHEET 5 AA5 5 ARG B 501 LEU B 502 1 O LEU B 502 N SER B 461 SHEET 1 AA6 2 SER B 59 HIS B 61 0 SHEET 2 AA6 2 VAL B 64 LYS B 66 -1 O LYS B 66 N SER B 59 SHEET 1 AA7 2 ALA B 157 ARG B 161 0 SHEET 2 AA7 2 GLU B 447 ALA B 451 -1 O VAL B 450 N PHE B 158 SHEET 1 AA8 2 THR B 218 PRO B 219 0 SHEET 2 AA8 2 GLU B 337 ILE B 338 -1 O ILE B 338 N THR B 218 CISPEP 1 GLU A 379 PRO A 380 0 2.20 CISPEP 2 GLU B 379 PRO B 380 0 -2.72 CRYST1 61.230 132.685 171.369 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 0.016332 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007537 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005835 0.00000