HEADER LIGASE 24-FEB-09 3GDE TITLE THE CLOSED CONFORMATION OF ATP-DEPENDENT DNA LIGASE FROM ARCHAEOGLOBUS TITLE 2 FULGIDUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP-DEPENDENT DNA LIGASE, POLYDEOXYRIBONUCLEOTIDE SYNTHASE COMPND 5 [ATP]; COMPND 6 EC: 6.5.1.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS; SOURCE 3 ORGANISM_TAXID: 2234; SOURCE 4 GENE: AF0623; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS ATP-DEPENDENT DNA LIGASE, DNA-BINDING DOMAIN, ADENYLATION DOMAIN, OB- KEYWDS 2 FOLD DOMAIN, ATP-BINDING, CELL CYCLE, CELL DIVISION, DNA DAMAGE, DNA KEYWDS 3 RECOMBINATION, DNA REPAIR, DNA REPLICATION, LIGASE, NUCLEOTIDE- KEYWDS 4 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.J.KIM,H.-W.KIM,O.KIM,H.S.KIM,S.J.LEE,S.W.SUH REVDAT 3 01-NOV-23 3GDE 1 REMARK SEQADV REVDAT 2 01-NOV-17 3GDE 1 REMARK REVDAT 1 15-DEC-09 3GDE 0 JRNL AUTH D.J.KIM,O.KIM,H.-W.KIM,H.S.KIM,S.J.LEE,S.W.SUH JRNL TITL ATP-DEPENDENT DNA LIGASE FROM ARCHAEOGLOBUS FULGIDUS JRNL TITL 2 DISPLAYS A TIGHTLY CLOSED CONFORMATION JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 65 544 2009 JRNL REFN ESSN 1744-3091 JRNL PMID 19478428 JRNL DOI 10.1107/S1744309109017485 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 36294 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4007 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2625 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 255 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4423 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 458 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.62000 REMARK 3 B22 (A**2) : 1.62000 REMARK 3 B33 (A**2) : -3.25000 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): 0.278 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.916 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4513 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6073 ; 1.314 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 549 ; 7.246 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;36.166 ;23.382 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 874 ;18.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;19.356 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 678 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3309 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2322 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3087 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 420 ; 0.153 ; 0.200 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): 57 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.187 ; 0.200 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): 2823 ; 0.683 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4418 ; 1.189 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1896 ; 1.622 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1655 ; 2.765 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3GDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40500 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2CFM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL, PH9.0, 0.4M SODIUM REMARK 280 DIHYDROGEN PHOSPHATE, 1.2M DIPOTASSIUM HYDROGEN PHOSPHATE, 10MM REMARK 280 MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 98.70800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.17750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.17750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.35400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.17750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.17750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 148.06200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.17750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.17750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 49.35400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.17750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.17750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 148.06200 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 0.00000 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 98.70800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 LYS A 320 REMARK 465 HIS A 321 REMARK 465 GLU A 551 REMARK 465 VAL A 552 REMARK 465 LYS A 553 REMARK 465 ARG A 554 REMARK 465 GLN A 555 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 OE2 GLU A 110 O HOH A 974 2.05 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 ARG A 411 NE - CZ - NH2 ANGL. DEV. = -3.3 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 GLU A 111 134.95 112.63 REMARK 500 HIS A 220 -3.14 84.37 REMARK 500 TRP A 259 129.83 -179.42 REMARK 500 ASP A 260 -79.44 179.59 REMARK 500 ASP A 343 62.80 38.51 REMARK 500 CYS A 346 14.60 -144.89 REMARK 500 PRO A 350 95.80 32.11 REMARK 500 SER A 365 -169.10 -128.73 REMARK 500 HIS A 394 -168.67 -105.44 REMARK 500 ARG A 411 75.99 -117.11 REMARK 500 ARG A 439 5.93 -66.06 REMARK 500 LYS A 497 -55.60 -158.45 REMARK 500 VAL A 525 -61.55 -98.06 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 LEU A 349 PRO A 350 81.10 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 PO4 A 556 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 557 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 558 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 559 DBREF 3GDE A 1 555 UNP O29632 DNLI_ARCFU 1 555 SEQADV 3GDE GLY A -2 UNP O29632 EXPRESSION TAG SEQADV 3GDE SER A -1 UNP O29632 EXPRESSION TAG SEQADV 3GDE HIS A 0 UNP O29632 EXPRESSION TAG SEQRES 1 A 558 GLY SER HIS MET LEU PHE ALA GLU PHE ALA GLU PHE CYS SEQRES 2 A 558 GLU ARG LEU GLU LYS ILE SER SER THR LEU GLU LEU THR SEQRES 3 A 558 ALA ARG ILE ALA ALA PHE LEU GLN LYS ILE GLU ASP GLU SEQRES 4 A 558 ARG ASP LEU TYR ASP VAL VAL LEU PHE ILE THR GLY LYS SEQRES 5 A 558 VAL TYR PRO PRO TRP ASP GLU ARG GLU LEU GLY VAL GLY SEQRES 6 A 558 ILE GLY LEU LEU TYR GLU ALA LEU GLU ASN VAL SER GLY SEQRES 7 A 558 VAL LYS ARG SER GLU ILE GLU SER MET ILE ARG GLU TYR SEQRES 8 A 558 GLY ASP LEU GLY LEU VAL ALA GLU GLN LEU ILE LYS LYS SEQRES 9 A 558 LYS LYS MET THR THR LEU ALA PHE GLU GLU LEU THR VAL SEQRES 10 A 558 ARG LYS VAL ARG GLU THR PHE ASP GLU ILE ALA SER LEU SEQRES 11 A 558 THR GLY GLU GLY SER MET LYS ARG LYS ILE MET LEU LEU SEQRES 12 A 558 THR GLY LEU TYR GLY LEU ALA THR PRO LEU GLU ALA ARG SEQRES 13 A 558 TYR LEU THR ARG LEU ILE LEU ASN GLU MET ARG LEU GLY SEQRES 14 A 558 VAL GLY GLU GLY ILE MET ARG ASP ALA ILE ALA ARG ALA SEQRES 15 A 558 PHE ARG ALA ASP PRO GLU THR VAL GLU ARG ALA TYR MET SEQRES 16 A 558 ILE THR ASN ASP LEU GLY ARG VAL ALA VAL VAL ALA LYS SEQRES 17 A 558 LYS GLU GLY GLU GLU GLY LEU ARG LYS MET LYS ILE GLU SEQRES 18 A 558 ILE HIS ILE PRO VAL ARG MET MET LEU ALA GLN VAL ALA SEQRES 19 A 558 GLU SER LEU GLU SER ALA VAL ARG GLU MET ARG THR ALA SEQRES 20 A 558 ALA VAL GLU TRP LYS PHE ASP GLY SER ARG VAL GLN VAL SEQRES 21 A 558 HIS TRP ASP GLY SER ARG VAL THR ILE TYR SER ARG ARG SEQRES 22 A 558 LEU GLU ASN VAL THR ASN ALA LEU PRO ASP ILE VAL GLU SEQRES 23 A 558 GLU ILE LYS LYS SER VAL LYS PRO GLY VAL ILE LEU ASP SEQRES 24 A 558 GLY GLU VAL ILE ALA VAL LYS GLU GLY LYS PRO MET PRO SEQRES 25 A 558 PHE GLN HIS VAL LEU ARG ARG PHE ARG ARG LYS HIS ASP SEQRES 26 A 558 VAL ALA LYS MET VAL GLU LYS ILE PRO LEU GLU ALA HIS SEQRES 27 A 558 PHE PHE ASP ILE LEU TYR HIS ASP GLY GLU CYS ILE ASP SEQRES 28 A 558 LEU PRO LEU ARG GLU ARG ARG LYS LEU LEU GLU SER ALA SEQRES 29 A 558 VAL ASN GLU SER GLU LYS ILE LYS LEU ALA LYS GLN ILE SEQRES 30 A 558 VAL THR ASP SER VAL ASP GLU VAL ARG LYS MET TYR ASP SEQRES 31 A 558 GLU ALA ILE SER ALA GLY HIS GLU GLY VAL MET ILE LYS SEQRES 32 A 558 LEU PRO SER SER PRO TYR ILE PRO GLY LYS ARG GLY LYS SEQRES 33 A 558 ASN TRP LEU LYS VAL LYS ALA ILE MET GLU THR LEU ASP SEQRES 34 A 558 LEU VAL VAL VAL GLY GLY GLU TRP GLY GLU GLY LYS ARG SEQRES 35 A 558 SER HIS TRP LEU SER SER PHE GLU LEU ALA CYS LEU ASP SEQRES 36 A 558 PRO VAL THR GLY LYS LEU LEU LYS VAL GLY ARG VAL ALA SEQRES 37 A 558 THR GLY PHE THR GLU GLU ASP LEU GLU GLU LEU THR GLU SEQRES 38 A 558 MET PHE ARG PRO LEU ILE VAL SER GLN GLN GLY LYS LYS SEQRES 39 A 558 VAL GLU PHE ILE PRO LYS TYR VAL PHE GLU VAL ALA TYR SEQRES 40 A 558 GLN GLU ILE GLN LYS SER PRO LYS TYR GLU SER GLY TYR SEQRES 41 A 558 ALA LEU ARG PHE PRO ARG PHE VAL ARG LEU ARG ASP ASP SEQRES 42 A 558 LYS ASP VAL ASP GLU ALA ASP THR ILE GLU ARG VAL GLU SEQRES 43 A 558 ASN LEU TYR LYS LEU GLN PHE GLU VAL LYS ARG GLN HET PO4 A 556 5 HET PO4 A 557 5 HET PO4 A 558 5 HET PO4 A 559 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 4(O4 P 3-) FORMUL 6 HOH *458(H2 O) HELIX 1 1 LEU A 2 GLU A 14 1 13 HELIX 2 2 SER A 18 LYS A 32 1 15 HELIX 3 3 ASP A 35 THR A 47 1 13 HELIX 4 4 GLY A 62 GLY A 75 1 14 HELIX 5 5 LYS A 77 GLY A 89 1 13 HELIX 6 6 ASP A 90 THR A 106 1 17 HELIX 7 7 THR A 113 LEU A 127 1 15 HELIX 8 8 GLY A 131 ALA A 147 1 17 HELIX 9 9 THR A 148 LEU A 160 1 13 HELIX 10 10 GLY A 168 PHE A 180 1 13 HELIX 11 11 ASP A 183 ASN A 195 1 13 HELIX 12 12 ASP A 196 LYS A 214 1 19 HELIX 13 13 SER A 233 MET A 241 1 9 HELIX 14 14 VAL A 274 ALA A 277 5 4 HELIX 15 15 LEU A 278 VAL A 289 1 12 HELIX 16 16 PRO A 309 ARG A 319 1 11 HELIX 17 17 VAL A 323 ILE A 330 1 8 HELIX 18 18 PRO A 350 VAL A 362 1 13 HELIX 19 19 SER A 378 ALA A 392 1 15 HELIX 20 20 LYS A 438 HIS A 441 5 4 HELIX 21 21 THR A 469 ARG A 481 1 13 HELIX 22 22 ASP A 532 ALA A 536 5 5 HELIX 23 23 THR A 538 LEU A 548 1 11 SHEET 1 A 5 LEU A 227 VAL A 230 0 SHEET 2 A 5 ARG A 411 LYS A 419 1 O LYS A 417 N GLN A 229 SHEET 3 A 5 GLY A 396 LYS A 400 -1 N ILE A 399 O LEU A 416 SHEET 4 A 5 ALA A 244 LYS A 249 -1 N ALA A 245 O LYS A 400 SHEET 5 A 5 GLN A 373 THR A 376 -1 O ILE A 374 N VAL A 246 SHEET 1 B 4 THR A 265 SER A 268 0 SHEET 2 B 4 SER A 253 TRP A 259 -1 N HIS A 258 O THR A 265 SHEET 3 B 4 VAL A 293 LYS A 303 -1 O VAL A 293 N TRP A 259 SHEET 4 B 4 LYS A 306 MET A 308 -1 O MET A 308 N ALA A 301 SHEET 1 C 5 THR A 265 SER A 268 0 SHEET 2 C 5 SER A 253 TRP A 259 -1 N HIS A 258 O THR A 265 SHEET 3 C 5 VAL A 293 LYS A 303 -1 O VAL A 293 N TRP A 259 SHEET 4 C 5 LEU A 332 HIS A 342 -1 O LEU A 340 N ILE A 294 SHEET 5 C 5 ILE A 368 LEU A 370 1 O LYS A 369 N ALA A 334 SHEET 1 D 5 LEU A 458 VAL A 464 0 SHEET 2 D 5 LEU A 443 LEU A 451 -1 N LEU A 448 O VAL A 461 SHEET 3 D 5 LEU A 425 TRP A 434 -1 N GLU A 433 O SER A 444 SHEET 4 D 5 LYS A 491 PHE A 494 -1 O PHE A 494 N VAL A 430 SHEET 5 D 5 ILE A 484 GLN A 488 -1 N GLN A 488 O LYS A 491 SHEET 1 E 5 LEU A 458 VAL A 464 0 SHEET 2 E 5 LEU A 443 LEU A 451 -1 N LEU A 448 O VAL A 461 SHEET 3 E 5 LEU A 425 TRP A 434 -1 N GLU A 433 O SER A 444 SHEET 4 E 5 VAL A 499 ALA A 503 -1 O VAL A 502 N LEU A 425 SHEET 5 E 5 ARG A 523 LEU A 527 -1 O ARG A 526 N GLU A 501 SHEET 1 F 2 GLU A 506 LYS A 509 0 SHEET 2 F 2 TYR A 517 ARG A 520 -1 O ARG A 520 N GLU A 506 CISPEP 1 TRP A 259 ASP A 260 0 -29.94 CISPEP 2 ASP A 260 GLY A 261 0 4.69 SITE 1 AC1 9 ARG A 269 ARG A 411 LYS A 417 PO4 A 557 SITE 2 AC1 9 HOH A 586 HOH A 587 HOH A 692 HOH A 890 SITE 3 AC1 9 HOH A 893 SITE 1 AC2 10 LYS A 249 GLU A 395 LYS A 417 LYS A 419 SITE 2 AC2 10 GLU A 423 PO4 A 556 PO4 A 558 HOH A 870 SITE 3 AC2 10 HOH A 971 HOH A1012 SITE 1 AC3 8 ARG A 528 LYS A 531 PO4 A 557 HOH A 730 SITE 2 AC3 8 HOH A 890 HOH A 904 HOH A 990 HOH A1012 SITE 1 AC4 4 GLN A 311 ARG A 526 HOH A 748 HOH A 866 CRYST1 94.355 94.355 197.416 90.00 90.00 90.00 P 41 21 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 0.010598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005065 0.00000