HEADER MOTOR PROTEIN 30-JUL-20 7CNB TITLE CRYSTAL STRUCTURE OF GP16 C-TERMINAL DOMAIN FROM BACILLUS VIRUS PHI29 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA PACKAGING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GP16, ATPASE GP16,GENE PRODUCT 16,GP16,PROTEIN P16; COMPND 5 EC: 3.6.4.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PHI29; SOURCE 3 ORGANISM_TAXID: 10756; SOURCE 4 GENE: 16; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRYSTAL STRUCTURE OF GP16 C-TERMINAL DOMAIN FROM BACILLUS VIRUS KEYWDS 2 PHI29, MOTOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.Y.OUYANG,A.F.U.H.SAEED REVDAT 4 27-MAR-24 7CNB 1 REMARK REVDAT 3 07-APR-21 7CNB 1 JRNL REVDAT 2 31-MAR-21 7CNB 1 JRNL REVDAT 1 24-MAR-21 7CNB 0 JRNL AUTH A.F.U.H.SAEED,C.CHAN,H.GUAN,B.GONG,P.GUO,X.CHENG,S.OUYANG JRNL TITL STRUCTURAL INSIGHTS INTO GP16 ATPASE IN THE BACTERIOPHAGE JRNL TITL 2 φ29 DNA PACKAGING MOTOR. JRNL REF BIOCHEMISTRY V. 60 886 2021 JRNL REFN ISSN 0006-2960 JRNL PMID 33689296 JRNL DOI 10.1021/ACS.BIOCHEM.0C00935 REMARK 2 REMARK 2 RESOLUTION. 2.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 5967 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.3790 - 2.3200 1.00 426 0 0.2910 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.219 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04000 REMARK 3 B22 (A**2) : 1.04000 REMARK 3 B33 (A**2) : -2.08000 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL 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 7CNB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1300017912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-18 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6004 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320 REMARK 200 RESOLUTION RANGE LOW (A) : 42.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.30 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 1.8 M AMMONIUM REMARK 280 SULFATE, 2% PEG MONOETHYL ETHER 550, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 67.92800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.96400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.89200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.92800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 101.89200 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 33.96400 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: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.96400 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 GLU A 24 CG CD OE1 OE2 REMARK 470 ARG A 104 CG CD NE CZ NH1 NH2 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 ASN A 107 CB - CA - C ANGL. DEV. = -13.5 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 SER A 19 70.28 47.76 REMARK 500 GLN A 20 39.77 -82.20 REMARK 500 ASN A 39 -117.21 49.23 REMARK 500 ASP A 74 40.60 74.67 REMARK 500 ILE A 123 76.40 -108.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 107 -10.73 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CNB A 18 124 UNP P11014 PKG16_BPPH2 226 332 SEQRES 1 A 107 ASP SER GLN VAL PHE ILE GLU LYS ARG SER LYS ASP SER SEQRES 2 A 107 LYS PHE VAL PHE SER ILE VAL TYR ASN GLY PHE THR LEU SEQRES 3 A 107 GLY VAL TRP VAL ASP VAL ASN GLN GLY LEU MET TYR ILE SEQRES 4 A 107 ASP THR ALA HIS ASP PRO SER THR LYS ASN VAL TYR THR SEQRES 5 A 107 LEU THR THR ASP ASP LEU ASN GLU ASN MET MET LEU ILE SEQRES 6 A 107 THR ASN TYR LYS ASN ASN TYR HIS LEU ARG LYS LEU ALA SEQRES 7 A 107 SER ALA PHE MET ASN GLY TYR LEU ARG PHE ASP ASN GLN SEQRES 8 A 107 VAL ILE ARG ASN ILE ALA TYR GLU LEU PHE ARG LYS MET SEQRES 9 A 107 ARG ILE GLN HELIX 1 AA1 ASN A 88 ASN A 100 1 13 HELIX 2 AA2 ASN A 107 MET A 121 1 15 SHEET 1 AA1 5 VAL A 67 LEU A 70 0 SHEET 2 AA1 5 LYS A 31 TYR A 38 1 N VAL A 37 O LEU A 70 SHEET 3 AA1 5 PHE A 41 ASP A 48 -1 O VAL A 45 N PHE A 34 SHEET 4 AA1 5 LEU A 53 ASP A 57 -1 O ASP A 57 N GLY A 44 SHEET 5 AA1 5 LEU A 103 PHE A 105 1 O ARG A 104 N MET A 54 CRYST1 42.682 42.682 135.856 90.00 90.00 90.00 P 41 2 2 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 0.023429 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023429 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007361 0.00000