HEADER VIRAL PROTEIN 21-MAY-04 1TD4 TITLE CRYSTAL STRUCTURE OF VSHP_BPP21 IN SPACE GROUP H3 WITH HIGH TITLE 2 RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAD DECORATION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEAD PROTEIN GPSHP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE P21; SOURCE 3 ORGANISM_TAXID: 10711; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SHP, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.CHANG,P.FORRER,D.OTT,A.WLODAWER,A.PLUECKTHUN REVDAT 4 20-SEP-23 1TD4 1 REMARK REVDAT 3 21-DEC-22 1TD4 1 SEQADV LINK REVDAT 2 24-FEB-09 1TD4 1 VERSN REVDAT 1 02-NOV-04 1TD4 0 JRNL AUTH P.FORRER,C.CHANG,D.OTT,A.WLODAWER,A.PLUECKTHUN JRNL TITL KINETIC STABILITY AND CRYSTAL STRUCTURE OF THE VIRAL CAPSID JRNL TITL 2 PROTEIN SHP. JRNL REF J.MOL.BIOL. V. 344 179 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15504410 JRNL DOI 10.1016/J.JMB.2004.09.030 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.138 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.126 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 669 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12731 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.125 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.113 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 569 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 10706 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 746 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 912.33 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 8311 REMARK 3 NUMBER OF RESTRAINTS : 8857 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.046 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.054 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.023 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.054 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 0.0326 REMARK 4 REMARK 4 1TD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022552. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1TD3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 18.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA ACETATE, PEG-MME 5000, MGCL2, PH REMARK 280 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K, PH 4.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.95450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.56219 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.81867 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 26.95450 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 15.56219 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.81867 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 26.95450 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 15.56219 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.81867 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 31.12438 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 51.63733 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 31.12438 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 51.63733 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 31.12438 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 51.63733 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: TRIMERIC 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 206 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 282 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 335 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 VAL A 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 THR A 4 REMARK 465 ILE A 5 REMARK 465 THR A 6 REMARK 465 GLU A 7 REMARK 465 GLN A 8 REMARK 465 ARG A 9 REMARK 465 ALA A 10 REMARK 465 GLU A 11 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 114 O 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 MET A 41 CG - SD - CE ANGL. DEV. = 14.9 DEGREES REMARK 500 TRP A 52 CD1 - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 TRP A 52 CG - CD1 - NE1 ANGL. DEV. = 7.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TD3 RELATED DB: PDB REMARK 900 SAME PROTEIN, C 2 SPACE GROUP DBREF 1TD4 A 0 114 UNP P36275 VSHP_BPP21 1 115 SEQADV 1TD4 DSN A 93 UNP P36275 SER 94 MODIFIED RESIDUE SEQRES 1 A 115 MET VAL THR LYS THR ILE THR GLU GLN ARG ALA GLU VAL SEQRES 2 A 115 ARG ILE PHE ALA GLY ASN ASP PRO ALA HIS THR ALA THR SEQRES 3 A 115 GLY SER SER GLY ILE SER SER PRO THR PRO ALA LEU THR SEQRES 4 A 115 PRO LEU MET LEU ASP GLU ALA THR GLY LYS LEU VAL VAL SEQRES 5 A 115 TRP ASP GLY GLN LYS ALA GLY SER ALA VAL GLY ILE LEU SEQRES 6 A 115 VAL LEU PRO LEU GLU GLY THR GLU THR ALA LEU THR TYR SEQRES 7 A 115 TYR LYS SER GLY THR PHE ALA THR GLU ALA ILE HIS TRP SEQRES 8 A 115 PRO GLU DSN VAL ASP GLU HIS LYS LYS ALA ASN ALA PHE SEQRES 9 A 115 ALA GLY SER ALA LEU SER HIS ALA ALA LEU PRO MODRES 1TD4 DSN A 93 SER D-SERINE HET DSN A 93 6 HETNAM DSN D-SERINE FORMUL 1 DSN C3 H7 N O3 FORMUL 2 HOH *166(H2 O) HELIX 1 1 GLU A 86 ILE A 88 5 3 HELIX 2 2 ASP A 95 ASN A 101 1 7 SHEET 1 A 5 THR A 23 SER A 27 0 SHEET 2 A 5 ALA A 74 TYR A 78 -1 O TYR A 77 N ALA A 24 SHEET 3 A 5 GLY A 62 LEU A 64 -1 N ILE A 63 O TYR A 78 SHEET 4 A 5 PRO A 39 LEU A 42 -1 N LEU A 40 O GLY A 62 SHEET 5 A 5 LEU A 49 VAL A 51 -1 O VAL A 50 N MET A 41 SHEET 1 B 2 SER A 80 ALA A 84 0 SHEET 2 B 2 ALA A 107 ALA A 111 1 O SER A 109 N PHE A 83 LINK C GLU A 92 N DSN A 93 1555 1555 1.31 LINK C DSN A 93 N VAL A 94 1555 1555 1.33 CISPEP 1 LEU A 113 PRO A 114 0 -7.33 CRYST1 53.909 53.909 77.456 90.00 90.00 120.00 H 3 9 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 0.018550 0.010710 0.000000 0.00000 SCALE2 0.000000 0.021419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012911 0.00000