HEADER TRANSFERASE, LYASE/DNA 20-JUN-12 4FO6
TITLE CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF POLYMERASE
TITLE 2 LAMBDA WITH A DATP ANALOG OPPOSITE A TEMPLATING T AND AN RCMP AT THE
TITLE 3 PRIMER TERMINUS.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE LAMBDA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: LOOP MUTANT OF DNA POLYMERASE LAMBDA;
COMPND 5 SYNONYM: POL LAMBDA, DNA POLYMERASE BETA-2, POL BETA2, DNA POLYMERASE
COMPND 6 KAPPA;
COMPND 7 EC: 2.7.7.7, 4.2.99.-;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES;
COMPND 10 MOL_ID: 2;
COMPND 11 MOLECULE: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3';
COMPND 12 CHAIN: T;
COMPND 13 ENGINEERED: YES;
COMPND 14 MOL_ID: 3;
COMPND 15 MOLECULE: 5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3';
COMPND 16 CHAIN: P;
COMPND 17 ENGINEERED: YES;
COMPND 18 MOL_ID: 4;
COMPND 19 MOLECULE: 5'-D(P*GP*CP*CP*G)-3';
COMPND 20 CHAIN: D;
COMPND 21 ENGINEERED: YES;
COMPND 22 MOL_ID: 5;
COMPND 23 MOLECULE: 5'-D(P*TP*AP*CP*TP*G)-3';
COMPND 24 CHAIN: H;
COMPND 25 ENGINEERED: YES;
COMPND 26 MOL_ID: 6;
COMPND 27 MOLECULE: 5'-D(P*CP*AP*GP*TP*A)-3';
COMPND 28 CHAIN: I;
COMPND 29 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: POLL;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 MOL_ID: 3;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 MOL_ID: 4;
SOURCE 13 SYNTHETIC: YES;
SOURCE 14 MOL_ID: 5;
SOURCE 15 SYNTHETIC: YES;
SOURCE 16 MOL_ID: 6
KEYWDS DNA POLYMERASE, TRANSFERASE, LYASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR R.A.GOSAVI,A.F.MOON,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK
REVDAT 2 13-SEP-23 4FO6 1 REMARK SEQADV LINK
REVDAT 1 11-JUL-12 4FO6 0
SPRSDE 11-JUL-12 4FO6 3UQ1
JRNL AUTH R.A.GOSAVI,A.F.MOON,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK
JRNL TITL THE CATALYTIC CYCLE FOR RIBONUCLEOTIDE INCORPORATION BY
JRNL TITL 2 HUMAN DNA POL LAMBDA
JRNL REF NUCLEIC ACIDS RES. V. 40 1 2012
JRNL REFN ISSN 0305-1048
JRNL PMID 22584622
JRNL DOI 10.1093/NAR/GKS413
REMARK 2
REMARK 2 RESOLUTION. 2.01 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_868)
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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.03
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1
REMARK 3 NUMBER OF REFLECTIONS : 32824
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.192
REMARK 3 R VALUE (WORKING SET) : 0.190
REMARK 3 FREE R VALUE : 0.231
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1603
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 24.0285 - 4.4555 0.98 3107 158 0.1883 0.2011
REMARK 3 2 4.4555 - 3.5401 1.00 3018 153 0.1543 0.1896
REMARK 3 3 3.5401 - 3.0937 1.00 3008 148 0.1816 0.2167
REMARK 3 4 3.0937 - 2.8113 1.00 2971 163 0.2064 0.2854
REMARK 3 5 2.8113 - 2.6100 1.00 2962 156 0.2013 0.2829
REMARK 3 6 2.6100 - 2.4563 0.99 2922 152 0.2034 0.2536
REMARK 3 7 2.4563 - 2.3334 0.99 2915 148 0.2017 0.2509
REMARK 3 8 2.3334 - 2.2319 0.97 2851 147 0.2124 0.2481
REMARK 3 9 2.2319 - 2.1460 0.93 2717 142 0.2313 0.2839
REMARK 3 10 2.1460 - 2.0720 0.84 2465 129 0.2315 0.2760
REMARK 3 11 2.0720 - 2.0073 0.75 2203 107 0.2274 0.2419
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.00
REMARK 3 SHRINKAGE RADIUS : 0.73
REMARK 3 K_SOL : 0.38
REMARK 3 B_SOL : 59.91
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.560
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.070
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 28.84
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -6.50070
REMARK 3 B22 (A**2) : 10.60810
REMARK 3 B33 (A**2) : -3.22100
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 : 0.011 3191
REMARK 3 ANGLE : 1.159 4471
REMARK 3 CHIRALITY : 0.071 501
REMARK 3 PLANARITY : 0.005 453
REMARK 3 DIHEDRAL : 11.139 886
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: NULL
REMARK 4
REMARK 4 4FO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-12.
REMARK 100 THE DEPOSITION ID IS D_1000073144.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-MAR-11
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 : APS
REMARK 200 BEAMLINE : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32824
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 25.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5
REMARK 200 DATA REDUNDANCY : 4.500
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
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) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07
REMARK 200 COMPLETENESS FOR SHELL (%) : 78.4
REMARK 200 DATA REDUNDANCY IN SHELL : 2.60
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.29700
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: PDB ENTRY 3MGI
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES PH 6.5, 9%(V/V) PEG400, 100MM
REMARK 280 KCL, 10MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-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 27.89000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.73500
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.82750
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.73500
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.89000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.82750
REMARK 290 SMTRY3 4 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: HEXAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D, H, I
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 ALA A 242
REMARK 465 GLN A 243
REMARK 465 PRO A 244
REMARK 465 SER A 245
REMARK 465 SER A 246
REMARK 465 GLN A 247
REMARK 465 LYS A 248
REMARK 465 ALA A 249
REMARK 465 THR A 250
REMARK 465 ASN A 251
REMARK 465 ARG A 438
REMARK 465 SER A 439
REMARK 465 HIS A 440
REMARK 465 ARG A 441
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 HIS A 252 CG ND1 CD2 CE1 NE2
REMARK 470 ILE A 256 CD1
REMARK 470 GLU A 258 CG CD OE1 OE2
REMARK 470 LYS A 259 NZ
REMARK 470 GLU A 261 CD OE1 OE2
REMARK 470 LYS A 265 CE NZ
REMARK 470 LYS A 281 CE NZ
REMARK 470 ASN A 284 OD1 ND2
REMARK 470 LYS A 291 CD CE NZ
REMARK 470 GLN A 297 CG CD OE1 NE2
REMARK 470 SER A 301 OG
REMARK 470 ILE A 302 CD1
REMARK 470 ILE A 314 CG1 CG2 CD1
REMARK 470 GLU A 318 CG CD OE1 OE2
REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 324 CD CE NZ
REMARK 470 HIS A 327 ND1 CD2 CE1 NE2
REMARK 470 GLU A 330 CD OE1 OE2
REMARK 470 LYS A 378 CE NZ
REMARK 470 GLU A 385 OE1 OE2
REMARK 470 GLU A 396 OE1 OE2
REMARK 470 LYS A 401 CD CE NZ
REMARK 470 GLN A 404 CD OE1 NE2
REMARK 470 SER A 408 OG
REMARK 470 ILE A 443 CG1 CG2 CD1
REMARK 470 ARG A 446 CZ NH1 NH2
REMARK 470 ASP A 449 OD1 OD2
REMARK 470 GLN A 453 CG CD OE1 NE2
REMARK 470 GLU A 470 CD OE1 OE2
REMARK 470 VAL A 545 CG1 CG2
REMARK 470 ARG A 568 NH1 NH2
REMARK 470 GLU A 569 OE1 OE2
REMARK 470 GLU A 572 OE1 OE2
REMARK 470 DC I 1 O5' C5'
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 DG D 1 P DG D 1 OP3 -0.125
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 DG T 2 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES
REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DG T 3 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES
REMARK 500 DT T 5 N3 - C4 - O4 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DT T 5 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES
REMARK 500 DG T 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DT T 7 O4' - C4' - C3' ANGL. DEV. = -5.0 DEGREES
REMARK 500 DT T 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 DT T 10 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES
REMARK 500 DG T 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG D 1 O4' - C1' - C2' ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG D 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DC H 9 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG H 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DC I 1 O4' - C1' - N1 ANGL. DEV. = 2.6 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 HIS A 255 42.60 -85.92
REMARK 500 CYS A 415 -143.93 -111.23
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 602 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 300 O
REMARK 620 2 ILE A 302 O 101.2
REMARK 620 3 ILE A 305 O 91.6 82.8
REMARK 620 4 DC D 3 OP1 169.3 88.4 94.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 605 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 339 O
REMARK 620 2 ILE A 341 O 101.0
REMARK 620 3 ALA A 344 O 89.7 87.9
REMARK 620 4 HOH A 704 O 88.9 89.3 176.5
REMARK 620 5 HOH A 728 O 69.9 167.8 84.0 98.5
REMARK 620 6 DA P 5 OP1 160.2 98.7 91.4 91.0 90.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 601 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 427 OD1
REMARK 620 2 ASP A 429 OD1 92.6
REMARK 620 3 F2A A 606 O2B 168.7 92.8
REMARK 620 4 F2A A 606 O1A 102.1 87.3 88.0
REMARK 620 5 F2A A 606 O3G 90.3 177.1 84.4 91.6
REMARK 620 6 HOH A 701 O 82.7 91.3 87.3 175.0 89.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 604 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 427 OD2
REMARK 620 2 ASP A 429 OD2 95.0
REMARK 620 3 ASP A 490 OD2 90.4 92.5
REMARK 620 4 F2A A 606 O1A 98.3 91.5 170.0
REMARK 620 5 HOH A 823 O 85.8 173.2 94.3 81.7
REMARK 620 6 C P 6 O3' 168.6 93.3 81.3 89.3 86.9
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 604
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 605
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F2A A 606
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3UPQ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF
REMARK 900 POLYMERASE LAMBDA WITH AN RATP ANALOG OPPOSITE A TEMPLATING T.
REMARK 900 RELATED ID: 3UQ0 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE POST-CATALYTIC PRODUCT COMPLEX OF
REMARK 900 POLYMERASE LAMBDA WITH AN RAMP AT THE PRIMER TERMINUS.
REMARK 900 RELATED ID: 3UQ2 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE POST-CATALYTIC PRODUCT COMPLEX OF
REMARK 900 POLYMERASE LAMBDA WITH AN RAMP INSERTED OPPOSITE A TEMPLATING G AND
REMARK 900 DAMP INSERTED OPPOSITE A TEMPLATING T AT THE PRIMER TERMINUS.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 AUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTION MUTANT, WITH
REMARK 999 RESIDUES SQEENGQQQ IN THE WILDTYPE SUBSTITUTED BY RESIDUES KGET.
REMARK 999 HOWEVER, THE RESIDUE NUMBERING WAS KEPT CONSISTENT WITH THE WT
REMARK 999 PROTEIN.
DBREF 4FO6 A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575
DBREF 4FO6 T 1 11 PDB 4FO6 4FO6 1 11
DBREF 4FO6 P 1 6 PDB 4FO6 4FO6 1 6
DBREF 4FO6 D 1 4 PDB 4FO6 4FO6 1 4
DBREF 4FO6 H 7 11 PDB 4FO6 4FO6 7 11
DBREF 4FO6 I 1 5 PDB 4FO6 4FO6 1 5
SEQADV 4FO6 LYS A 463 UNP Q9UGP5 SER 463 SEE REMARK 999
SEQADV 4FO6 GLY A 464 UNP Q9UGP5 GLN 464 SEE REMARK 999
SEQADV 4FO6 GLU A 470 UNP Q9UGP5 GLN 470 SEE REMARK 999
SEQADV 4FO6 THR A 471 UNP Q9UGP5 GLN 471 SEE REMARK 999
SEQADV 4FO6 ALA A 543 UNP Q9UGP5 CYS 543 ENGINEERED MUTATION
SEQRES 1 A 329 ALA GLN PRO SER SER GLN LYS ALA THR ASN HIS ASN LEU
SEQRES 2 A 329 HIS ILE THR GLU LYS LEU GLU VAL LEU ALA LYS ALA TYR
SEQRES 3 A 329 SER VAL GLN GLY ASP LYS TRP ARG ALA LEU GLY TYR ALA
SEQRES 4 A 329 LYS ALA ILE ASN ALA LEU LYS SER PHE HIS LYS PRO VAL
SEQRES 5 A 329 THR SER TYR GLN GLU ALA CYS SER ILE PRO GLY ILE GLY
SEQRES 6 A 329 LYS ARG MET ALA GLU LYS ILE ILE GLU ILE LEU GLU SER
SEQRES 7 A 329 GLY HIS LEU ARG LYS LEU ASP HIS ILE SER GLU SER VAL
SEQRES 8 A 329 PRO VAL LEU GLU LEU PHE SER ASN ILE TRP GLY ALA GLY
SEQRES 9 A 329 THR LYS THR ALA GLN MET TRP TYR GLN GLN GLY PHE ARG
SEQRES 10 A 329 SER LEU GLU ASP ILE ARG SER GLN ALA SER LEU THR THR
SEQRES 11 A 329 GLN GLN ALA ILE GLY LEU LYS HIS TYR SER ASP PHE LEU
SEQRES 12 A 329 GLU ARG MET PRO ARG GLU GLU ALA THR GLU ILE GLU GLN
SEQRES 13 A 329 THR VAL GLN LYS ALA ALA GLN ALA PHE ASN SER GLY LEU
SEQRES 14 A 329 LEU CYS VAL ALA CYS GLY SER TYR ARG ARG GLY LYS ALA
SEQRES 15 A 329 THR CYS GLY ASP VAL ASP VAL LEU ILE THR HIS PRO ASP
SEQRES 16 A 329 GLY ARG SER HIS ARG GLY ILE PHE SER ARG LEU LEU ASP
SEQRES 17 A 329 SER LEU ARG GLN GLU GLY PHE LEU THR ASP ASP LEU VAL
SEQRES 18 A 329 LYS GLY GLU THR LYS TYR LEU GLY VAL CYS ARG LEU PRO
SEQRES 19 A 329 GLY PRO GLY ARG ARG HIS ARG ARG LEU ASP ILE ILE VAL
SEQRES 20 A 329 VAL PRO TYR SER GLU PHE ALA CYS ALA LEU LEU TYR PHE
SEQRES 21 A 329 THR GLY SER ALA HIS PHE ASN ARG SER MET ARG ALA LEU
SEQRES 22 A 329 ALA LYS THR LYS GLY MET SER LEU SER GLU HIS ALA LEU
SEQRES 23 A 329 SER THR ALA VAL VAL ARG ASN THR HIS GLY ALA LYS VAL
SEQRES 24 A 329 GLY PRO GLY ARG VAL LEU PRO THR PRO THR GLU LYS ASP
SEQRES 25 A 329 VAL PHE ARG LEU LEU GLY LEU PRO TYR ARG GLU PRO ALA
SEQRES 26 A 329 GLU ARG ASP TRP
SEQRES 1 T 11 DC DG DG DC DT DG DT DA DC DT DG
SEQRES 1 P 6 DC DA DG DT DA C
SEQRES 1 D 4 DG DC DC DG
SEQRES 1 H 5 DT DA DC DT DG
SEQRES 1 I 5 DC DA DG DT DA
HET MG A 601 1
HET NA A 602 1
HET CL A 603 1
HET MN A 604 1
HET NA A 605 1
HET F2A A 606 30
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
HETNAM CL CHLORIDE ION
HETNAM MN MANGANESE (II) ION
HETNAM F2A 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 F2A PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE
FORMUL 7 MG MG 2+
FORMUL 8 NA 2(NA 1+)
FORMUL 9 CL CL 1-
FORMUL 10 MN MN 2+
FORMUL 12 F2A C11 H18 N5 O11 P3
FORMUL 13 HOH *212(H2 O)
HELIX 1 1 ILE A 256 GLN A 270 1 15
HELIX 2 2 ASP A 272 SER A 288 1 17
HELIX 3 3 SER A 295 CYS A 300 1 6
HELIX 4 4 GLY A 306 GLY A 320 1 15
HELIX 5 5 LEU A 322 HIS A 327 1 6
HELIX 6 6 SER A 331 ASN A 340 1 10
HELIX 7 7 GLY A 345 GLN A 355 1 11
HELIX 8 8 SER A 359 ALA A 367 1 9
HELIX 9 9 THR A 370 HIS A 379 1 10
HELIX 10 10 SER A 381 GLU A 385 5 5
HELIX 11 11 ARG A 389 ALA A 405 1 17
HELIX 12 12 CYS A 415 ARG A 420 1 6
HELIX 13 13 ILE A 443 GLU A 454 1 12
HELIX 14 14 GLU A 498 GLY A 508 1 11
HELIX 15 15 SER A 509 LYS A 523 1 15
HELIX 16 16 THR A 555 LEU A 563 1 9
HELIX 17 17 GLU A 569 ASP A 574 5 6
SHEET 1 A 2 MET A 387 PRO A 388 0
SHEET 2 A 2 THR A 424 CYS A 425 -1 O CYS A 425 N MET A 387
SHEET 1 B 5 LEU A 411 ALA A 414 0
SHEET 2 B 5 VAL A 428 HIS A 434 -1 O LEU A 431 N VAL A 413
SHEET 3 B 5 ARG A 487 PRO A 495 1 O ASP A 490 N VAL A 430
SHEET 4 B 5 LYS A 472 CYS A 477 -1 N CYS A 477 O ARG A 487
SHEET 5 B 5 LEU A 457 LYS A 463 -1 N LEU A 461 O LEU A 474
SHEET 1 C 3 SER A 526 LEU A 527 0
SHEET 2 C 3 LEU A 532 THR A 534 -1 O SER A 533 N SER A 526
SHEET 3 C 3 ARG A 549 VAL A 550 -1 O ARG A 549 N THR A 534
SHEET 1 D 2 VAL A 537 ARG A 538 0
SHEET 2 D 2 LYS A 544 GLY A 546 -1 O VAL A 545 N VAL A 537
LINK O CYS A 300 NA NA A 602 1555 1555 2.94
LINK O ILE A 302 NA NA A 602 1555 1555 2.40
LINK O ILE A 305 NA NA A 602 1555 1555 2.84
LINK O SER A 339 NA NA A 605 1555 1555 2.39
LINK O ILE A 341 NA NA A 605 1555 1555 2.41
LINK O ALA A 344 NA NA A 605 1555 1555 2.36
LINK OD1 ASP A 427 MG MG A 601 1555 1555 1.99
LINK OD2 ASP A 427 MN MN A 604 1555 1555 2.03
LINK OD1 ASP A 429 MG MG A 601 1555 1555 1.96
LINK OD2 ASP A 429 MN MN A 604 1555 1555 2.15
LINK OD2 ASP A 490 MN MN A 604 1555 1555 2.16
LINK MG MG A 601 O2B F2A A 606 1555 1555 2.05
LINK MG MG A 601 O1A F2A A 606 1555 1555 2.14
LINK MG MG A 601 O3G F2A A 606 1555 1555 2.19
LINK MG MG A 601 O HOH A 701 1555 1555 2.08
LINK NA NA A 602 OP1 DC D 3 1555 1555 3.17
LINK MN MN A 604 O1A F2A A 606 1555 1555 2.29
LINK MN MN A 604 O HOH A 823 1555 1555 2.21
LINK MN MN A 604 O3' C P 6 1555 1555 2.19
LINK NA NA A 605 O HOH A 704 1555 1555 2.42
LINK NA NA A 605 O HOH A 728 1555 1555 2.43
LINK NA NA A 605 OP1 DA P 5 1555 1555 2.49
CISPEP 1 GLY A 508 SER A 509 0 7.79
SITE 1 AC1 5 ASP A 427 ASP A 429 MN A 604 F2A A 606
SITE 2 AC1 5 HOH A 701
SITE 1 AC2 4 CYS A 300 ILE A 302 ILE A 305 DC D 3
SITE 1 AC3 3 ARG A 517 GLU A 529 DG T 6
SITE 1 AC4 7 ASP A 427 ASP A 429 ASP A 490 MG A 601
SITE 2 AC4 7 F2A A 606 HOH A 823 C P 6
SITE 1 AC5 6 SER A 339 ILE A 341 ALA A 344 HOH A 704
SITE 2 AC5 6 HOH A 728 DA P 5
SITE 1 AC6 25 ARG A 386 GLY A 416 SER A 417 ARG A 420
SITE 2 AC6 25 CYS A 425 GLY A 426 ASP A 427 ASP A 429
SITE 3 AC6 25 TYR A 505 PHE A 506 THR A 507 GLY A 508
SITE 4 AC6 25 ALA A 510 ASN A 513 MG A 601 MN A 604
SITE 5 AC6 25 HOH A 701 HOH A 703 HOH A 735 HOH A 737
SITE 6 AC6 25 HOH A 782 HOH A 823 C P 6 DT T 5
SITE 7 AC6 25 DG T 6
CRYST1 55.780 63.655 141.470 90.00 90.00 90.00 P 21 21 21 4
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 0.017928 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015710 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007069 0.00000