HEADER REPLICATION 13-JUL-04 1U0J TITLE CRYSTAL STRUCTURE OF AAV2 REP40-ADP COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPLICATION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HELICASE DOMAIN 225-490; COMPND 5 SYNONYM: NONCAPSID PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ADENO-ASSOCIATED VIRUS - 2; SOURCE 3 ORGANISM_TAXID: 10804; SOURCE 4 GENE: REP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(PLYSS)DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-15B KEYWDS AAA+ PROTEIN, P-LOOP ATPASES, HELICASE, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR J.A.JAMES,A.K.AGGARWAL,R.M.LINDEN,C.R.ESCALANTE REVDAT 5 23-AUG-23 1U0J 1 REMARK SEQADV REVDAT 4 31-JAN-18 1U0J 1 REMARK REVDAT 3 24-FEB-09 1U0J 1 VERSN REVDAT 2 07-SEP-04 1U0J 1 JRNL REVDAT 1 24-AUG-04 1U0J 0 JRNL AUTH J.A.JAMES,A.K.AGGARWAL,R.M.LINDEN,C.R.ESCALANTE JRNL TITL STRUCTURE OF ADENO-ASSOCIATED VIRUS TYPE 2 REP40-ADP JRNL TITL 2 COMPLEX: INSIGHT INTO NUCLEOTIDE RECOGNITION AND CATALYSIS JRNL TITL 3 BY SUPERFAMILY 3 HELICASES JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 12455 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15310852 JRNL DOI 10.1073/PNAS.0403454101 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 279330.810 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.2 REMARK 3 NUMBER OF REFLECTIONS : 13428 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 SET) : 0.192 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1445 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 182 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2044 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.88000 REMARK 3 B22 (A**2) : 4.88000 REMARK 3 B33 (A**2) : -9.76000 REMARK 3 B12 (A**2) : 6.27000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 2.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.040 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.060 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.570 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.950 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 30.93 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ADP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U0J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 109 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : CHANNEL-CUT CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS - B4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NOVEL_R REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15662 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 50.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.06200 REMARK 200 R SYM FOR SHELL (I) : 0.06200 REMARK 200 FOR SHELL : 17.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1S9H (CHAIN B) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, SODIUM ACETATE, MGCL2, TRIS, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 4K, REMARK 280 TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 63.59733 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 31.79867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.69800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.89933 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 79.49667 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: MONOMERIC 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 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 ASP A 402 REMARK 465 GLN A 403 REMARK 465 LYS A 404 REMARK 465 CYS A 405 REMARK 465 LYS A 406 REMARK 465 SER A 407 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 GLN A 262 CG CD OE1 NE2 REMARK 470 GLU A 362 CG CD OE1 OE2 REMARK 470 PHE A 364 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 398 CG CD CE NZ REMARK 470 ARG A 452 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 453 CG CD NE CZ NH1 NH2 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 O SER A 408 N ALA A 409 1.60 REMARK 500 O ASN A 254 N ALA A 255 1.67 REMARK 500 N6 ADP A 491 O HOH A 40 2.11 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 OE2 GLU A 226 OE2 GLU A 449 2654 1.62 REMARK 500 OE2 GLU A 226 CD GLU A 449 2654 2.08 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 ASN A 254 C ALA A 255 N -0.359 REMARK 500 SER A 257 CB SER A 257 OG -0.086 REMARK 500 ARG A 260 CB ARG A 260 CG -0.500 REMARK 500 SER A 408 C ALA A 409 N -0.361 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 ASN A 254 CA - C - N ANGL. DEV. = 18.7 DEGREES REMARK 500 ASN A 254 O - C - N ANGL. DEV. = -25.0 DEGREES REMARK 500 SER A 257 CA - CB - OG ANGL. DEV. = 27.0 DEGREES REMARK 500 SER A 259 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 260 CA - CB - CG ANGL. DEV. = 55.2 DEGREES REMARK 500 ARG A 260 CB - CG - CD ANGL. DEV. = -32.0 DEGREES REMARK 500 PRO A 289 CA - N - CD ANGL. DEV. = -23.2 DEGREES REMARK 500 SER A 408 CA - C - N ANGL. DEV. = 27.8 DEGREES REMARK 500 SER A 408 O - C - N ANGL. DEV. = -30.1 DEGREES REMARK 500 ALA A 409 C - N - CA ANGL. DEV. = 47.8 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 ASP A 246 59.51 -148.87 REMARK 500 ASN A 254 38.11 -80.27 REMARK 500 PHE A 324 36.88 -99.54 REMARK 500 ASN A 423 92.90 -69.99 REMARK 500 HIS A 476 34.55 -140.04 REMARK 500 LYS A 488 75.19 -106.92 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 SER A 408 ALA A 409 -80.88 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 254 -22.85 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 ADP A 491 DBREF 1U0J A 225 490 UNP P03132 VNCA_AAV2 225 490 SEQADV 1U0J GLY A 224 UNP P03132 CLONING ARTIFACT SEQRES 1 A 267 GLY MET GLU LEU VAL GLY TRP LEU VAL ASP LYS GLY ILE SEQRES 2 A 267 THR SER GLU LYS GLN TRP ILE GLN GLU ASP GLN ALA SER SEQRES 3 A 267 TYR ILE SER PHE ASN ALA ALA SER ASN SER ARG SER GLN SEQRES 4 A 267 ILE LYS ALA ALA LEU ASP ASN ALA GLY LYS ILE MET SER SEQRES 5 A 267 LEU THR LYS THR ALA PRO ASP TYR LEU VAL GLY GLN GLN SEQRES 6 A 267 PRO VAL GLU ASP ILE SER SER ASN ARG ILE TYR LYS ILE SEQRES 7 A 267 LEU GLU LEU ASN GLY TYR ASP PRO GLN TYR ALA ALA SER SEQRES 8 A 267 VAL PHE LEU GLY TRP ALA THR LYS LYS PHE GLY LYS ARG SEQRES 9 A 267 ASN THR ILE TRP LEU PHE GLY PRO ALA THR THR GLY LYS SEQRES 10 A 267 THR ASN ILE ALA GLU ALA ILE ALA HIS THR VAL PRO PHE SEQRES 11 A 267 TYR GLY CYS VAL ASN TRP THR ASN GLU ASN PHE PRO PHE SEQRES 12 A 267 ASN ASP CYS VAL ASP LYS MET VAL ILE TRP TRP GLU GLU SEQRES 13 A 267 GLY LYS MET THR ALA LYS VAL VAL GLU SER ALA LYS ALA SEQRES 14 A 267 ILE LEU GLY GLY SER LYS VAL ARG VAL ASP GLN LYS CYS SEQRES 15 A 267 LYS SER SER ALA GLN ILE ASP PRO THR PRO VAL ILE VAL SEQRES 16 A 267 THR SER ASN THR ASN MET CYS ALA VAL ILE ASP GLY ASN SEQRES 17 A 267 SER THR THR PHE GLU HIS GLN GLN PRO LEU GLN ASP ARG SEQRES 18 A 267 MET PHE LYS PHE GLU LEU THR ARG ARG LEU ASP HIS ASP SEQRES 19 A 267 PHE GLY LYS VAL THR LYS GLN GLU VAL LYS ASP PHE PHE SEQRES 20 A 267 ARG TRP ALA LYS ASP HIS VAL VAL GLU VAL GLU HIS GLU SEQRES 21 A 267 PHE TYR VAL LYS LYS GLY GLY HET ADP A 491 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 HOH *212(H2 O) HELIX 1 1 GLY A 224 GLY A 235 1 12 HELIX 2 2 SER A 238 ALA A 255 1 18 HELIX 3 3 SER A 259 LYS A 278 1 20 HELIX 4 4 THR A 279 VAL A 285 1 7 HELIX 5 5 ASP A 292 SER A 295 5 4 HELIX 6 6 ASN A 296 ASN A 305 1 10 HELIX 7 7 ASP A 308 THR A 321 1 14 HELIX 8 8 GLY A 339 VAL A 351 1 13 HELIX 9 9 PHE A 366 VAL A 370 5 5 HELIX 10 10 VAL A 386 GLY A 395 1 10 HELIX 11 11 HIS A 437 ASP A 443 1 7 HELIX 12 12 THR A 462 HIS A 476 1 15 SHEET 1 A 5 TYR A 354 CYS A 356 0 SHEET 2 A 5 VAL A 374 TRP A 377 1 O TRP A 376 N GLY A 355 SHEET 3 A 5 VAL A 416 SER A 420 1 O ILE A 417 N ILE A 375 SHEET 4 A 5 THR A 329 PHE A 333 1 N LEU A 332 O VAL A 418 SHEET 5 A 5 MET A 445 GLU A 449 1 O PHE A 446 N TRP A 331 SHEET 1 B 3 MET A 382 THR A 383 0 SHEET 2 B 3 VAL A 427 ASP A 429 1 O ILE A 428 N MET A 382 SHEET 3 B 3 SER A 432 THR A 434 -1 O SER A 432 N ASP A 429 SHEET 1 C 2 VAL A 399 ARG A 400 0 SHEET 2 C 2 GLN A 410 ILE A 411 -1 O ILE A 411 N VAL A 399 SITE 1 AC1 19 HOH A 26 HOH A 40 HOH A 78 HOH A 93 SITE 2 AC1 19 HOH A 110 HOH A 112 ALA A 336 THR A 337 SITE 3 AC1 19 THR A 338 GLY A 339 LYS A 340 THR A 341 SITE 4 AC1 19 ASN A 342 LEU A 454 ASP A 455 HIS A 456 SITE 5 AC1 19 PHE A 458 GLY A 459 LYS A 460 CRYST1 71.000 71.000 95.396 90.00 90.00 120.00 P 65 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 0.014085 0.008132 0.000000 0.00000 SCALE2 0.000000 0.016263 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010483 0.00000