HEADER VIRAL PROTEIN 18-NOV-99 1C5E TITLE BACTERIOPHAGE LAMBDA HEAD PROTEIN D COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAD DECORATION PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: GPD, MAJOR CAPSID PROTEIN D; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 3 ORGANISM_TAXID: 10710 KEYWDS BACTERIOPHAGE LAMBDA, HEAD PROTEIN D, PROTEIN CRYSTAL STRUCTURE, KEYWDS 2 VIRUS ASSEMBLY, PHAGE DISPLAY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.YANG,P.FORRER,Z.DAUTER,A.PLUCKTHUN,A.WLODAWER REVDAT 6 27-DEC-23 1C5E 1 REMARK REVDAT 5 13-JUL-11 1C5E 1 VERSN REVDAT 4 24-FEB-09 1C5E 1 VERSN REVDAT 3 01-APR-03 1C5E 1 JRNL REVDAT 2 26-SEP-01 1C5E 3 ATOM REVDAT 1 08-MAR-00 1C5E 0 JRNL AUTH F.YANG,P.FORRER,Z.DAUTER,J.F.CONWAY,N.CHENG,M.E.CERRITELLI, JRNL AUTH 2 A.C.STEVEN,A.PLUCKTHUN,A.WLODAWER JRNL TITL NOVEL FOLD AND CAPSID-BINDING PROPERTIES OF THE LAMBDA-PHAGE JRNL TITL 2 DISPLAY PLATFORM PROTEIN GPD. JRNL REF NAT.STRUCT.BIOL. V. 7 230 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 10700283 JRNL DOI 10.1038/73347 REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.098 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.099 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.133 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5346 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 104260 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.092 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.093 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.126 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 4879 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 95164 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2073 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 309 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2394.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2051.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 21691 REMARK 3 NUMBER OF RESTRAINTS : 26304 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.087 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.087 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.118 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.047 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.119 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) REMARK 4 REMARK 4 1C5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000001358. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 109996 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 4.60000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 25.6000 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXL-97 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 4000, 0.1 M BIS-TRIS PH 6.5, REMARK 280 10 % GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.53500 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 ARG A 44 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 44 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 81 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG B 44 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG C 81 NE - CZ - NH2 ANGL. DEV. = 4.2 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 MET A 34 9.89 86.23 REMARK 500 MET B 34 10.44 86.66 REMARK 500 MET C 34 9.51 87.17 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 GOL A 599 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 600 DBREF 1C5E A 15 109 UNP P03712 VCAD_LAMBD 16 110 DBREF 1C5E B 15 109 UNP P03712 VCAD_LAMBD 16 110 DBREF 1C5E C 15 109 UNP P03712 VCAD_LAMBD 16 110 SEQRES 1 A 95 SER ASP PRO ALA HIS THR ALA THR ALA PRO GLY GLY LEU SEQRES 2 A 95 SER ALA LYS ALA PRO ALA MET THR PRO LEU MET LEU ASP SEQRES 3 A 95 THR SER SER ARG LYS LEU VAL ALA TRP ASP GLY THR THR SEQRES 4 A 95 ASP GLY ALA ALA VAL GLY ILE LEU ALA VAL ALA ALA ASP SEQRES 5 A 95 GLN THR SER THR THR LEU THR PHE TYR LYS SER GLY THR SEQRES 6 A 95 PHE ARG TYR GLU ASP VAL LEU TRP PRO GLU ALA ALA SER SEQRES 7 A 95 ASP GLU THR LYS LYS ARG THR ALA PHE ALA GLY THR ALA SEQRES 8 A 95 ILE SER ILE VAL SEQRES 1 B 95 SER ASP PRO ALA HIS THR ALA THR ALA PRO GLY GLY LEU SEQRES 2 B 95 SER ALA LYS ALA PRO ALA MET THR PRO LEU MET LEU ASP SEQRES 3 B 95 THR SER SER ARG LYS LEU VAL ALA TRP ASP GLY THR THR SEQRES 4 B 95 ASP GLY ALA ALA VAL GLY ILE LEU ALA VAL ALA ALA ASP SEQRES 5 B 95 GLN THR SER THR THR LEU THR PHE TYR LYS SER GLY THR SEQRES 6 B 95 PHE ARG TYR GLU ASP VAL LEU TRP PRO GLU ALA ALA SER SEQRES 7 B 95 ASP GLU THR LYS LYS ARG THR ALA PHE ALA GLY THR ALA SEQRES 8 B 95 ILE SER ILE VAL SEQRES 1 C 95 SER ASP PRO ALA HIS THR ALA THR ALA PRO GLY GLY LEU SEQRES 2 C 95 SER ALA LYS ALA PRO ALA MET THR PRO LEU MET LEU ASP SEQRES 3 C 95 THR SER SER ARG LYS LEU VAL ALA TRP ASP GLY THR THR SEQRES 4 C 95 ASP GLY ALA ALA VAL GLY ILE LEU ALA VAL ALA ALA ASP SEQRES 5 C 95 GLN THR SER THR THR LEU THR PHE TYR LYS SER GLY THR SEQRES 6 C 95 PHE ARG TYR GLU ASP VAL LEU TRP PRO GLU ALA ALA SER SEQRES 7 C 95 ASP GLU THR LYS LYS ARG THR ALA PHE ALA GLY THR ALA SEQRES 8 C 95 ILE SER ILE VAL HET GOL A 599 6 HET GOL C 600 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *309(H2 O) HELIX 1 1 GLU A 94 ARG A 98 1 5 HELIX 2 2 GLU B 94 ARG B 98 1 5 HELIX 3 3 GLU C 94 ARG C 98 1 5 SHEET 1 A 2 THR A 20 PRO A 24 0 SHEET 2 A 2 THR A 71 TYR A 75 -1 N PHE A 74 O ALA A 21 SHEET 1 B 3 LEU A 46 ALA A 48 0 SHEET 2 B 3 PRO A 36 LEU A 39 -1 N MET A 38 O VAL A 47 SHEET 3 B 3 ALA A 57 ILE A 60 -1 N GLY A 59 O LEU A 37 SHEET 1 C 2 SER A 77 ARG A 81 0 SHEET 2 C 2 ALA A 105 VAL A 109 1 N ALA A 105 O GLY A 78 SHEET 1 D 2 THR B 20 PRO B 24 0 SHEET 2 D 2 THR B 71 TYR B 75 -1 N PHE B 74 O ALA B 21 SHEET 1 E 3 LEU B 46 ALA B 48 0 SHEET 2 E 3 PRO B 36 LEU B 39 -1 N MET B 38 O VAL B 47 SHEET 3 E 3 ALA B 57 ILE B 60 -1 N GLY B 59 O LEU B 37 SHEET 1 F 2 SER B 77 ARG B 81 0 SHEET 2 F 2 ALA B 105 VAL B 109 1 N ALA B 105 O GLY B 78 SHEET 1 G 2 THR C 20 PRO C 24 0 SHEET 2 G 2 THR C 71 TYR C 75 -1 N PHE C 74 O ALA C 21 SHEET 1 H 3 LEU C 46 ALA C 48 0 SHEET 2 H 3 PRO C 36 LEU C 39 -1 N MET C 38 O VAL C 47 SHEET 3 H 3 ALA C 57 ILE C 60 -1 N GLY C 59 O LEU C 37 SHEET 1 I 2 SER C 77 ARG C 81 0 SHEET 2 I 2 ALA C 105 VAL C 109 1 N ALA C 105 O GLY C 78 SITE 1 AC1 9 VAL A 63 ALA A 64 ALA A 65 THR A 71 SITE 2 AC1 9 LEU A 72 THR A 73 HOH A 904 HOH A 908 SITE 3 AC1 9 HOH B 624 SITE 1 AC2 9 HOH A 638 LEU C 61 VAL C 63 ALA C 65 SITE 2 AC2 9 THR C 71 LEU C 72 THR C 73 HOH C 906 SITE 3 AC2 9 HOH C 909 CRYST1 45.580 69.070 45.590 90.00 104.32 90.00 P 1 21 1 6 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 0.021939 0.000000 0.005600 0.00000 SCALE2 0.000000 0.014478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022638 0.00000 MTRIX1 1 -0.254172 0.010299 0.967104 29.27348 1 MTRIX2 1 -0.911654 0.331324 -0.243127 35.04161 1 MTRIX3 1 -0.322929 -0.943461 -0.074824 26.58102 1 MTRIX1 2 -0.226471 -0.922287 -0.313205 48.23424 1 MTRIX2 2 -0.001972 0.321993 -0.946740 13.84381 1 MTRIX3 2 0.974016 -0.213792 -0.074740 -19.08689 1