PDB Short entry for 3UPQ HEADER TRANSFERASE, LYASE/DNA 18-NOV-11 3UPQ TITLE CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF POLYMERASE TITLE 2 LAMBDA WITH AN RATP ANALOG OPPOSITE A TEMPLATING T. 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*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 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 KEYWDS DNA, POLYMERASE, DNA POLYMERASE LAMBDA, RIBONUCLEOTIDE INCORPORATION, KEYWDS 2 TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.A.GOSAVI,A.F.MOON,T.A.KUNKEL,L.C.PEDERSEN,K.BEBENEK REVDAT 4 13-SEP-23 3UPQ 1 REMARK LINK REVDAT 3 26-SEP-12 3UPQ 1 JRNL REVDAT 2 18-JUL-12 3UPQ 1 JRNL REVDAT 1 23-MAY-12 3UPQ 0 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 7518 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22584622 JRNL DOI 10.1093/NAR/GKS413 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 36538 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1787 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 27.4470 - 4.5785 1.00 2919 145 0.1995 0.2225 REMARK 3 2 4.5785 - 3.6368 1.00 2775 154 0.1772 0.2371 REMARK 3 3 3.6368 - 3.1779 1.00 2761 134 0.2070 0.2355 REMARK 3 4 3.1779 - 2.8876 1.00 2723 143 0.2252 0.2313 REMARK 3 5 2.8876 - 2.6809 1.00 2700 136 0.2268 0.2719 REMARK 3 6 2.6809 - 2.5229 1.00 2699 140 0.2177 0.2649 REMARK 3 7 2.5229 - 2.3966 0.99 2693 140 0.2202 0.2379 REMARK 3 8 2.3966 - 2.2924 0.99 2647 138 0.2241 0.3168 REMARK 3 9 2.2924 - 2.2042 0.97 2624 135 0.2220 0.2294 REMARK 3 10 2.2042 - 2.1281 0.98 2617 133 0.2104 0.2639 REMARK 3 11 2.1281 - 2.0616 0.97 2611 132 0.2141 0.2305 REMARK 3 12 2.0616 - 2.0027 0.95 2545 132 0.2171 0.2741 REMARK 3 13 2.0027 - 1.9500 0.90 2437 125 0.2401 0.2713 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 42.19 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.80120 REMARK 3 B22 (A**2) : 5.57620 REMARK 3 B33 (A**2) : 0.22500 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 : 0.010 2912 REMARK 3 ANGLE : 1.069 4075 REMARK 3 CHIRALITY : 0.062 450 REMARK 3 PLANARITY : 0.004 441 REMARK 3 DIHEDRAL : 12.836 855 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 3UPQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000069054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM 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 : GRAPHITE 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 : 37285 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3MGI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NA HEPES PH 7.5, 1.0M LITHIUM REMARK 280 SULFATE, 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 27.98750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.98500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.98500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.98750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.83000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 VAL A 537 REMARK 465 ARG A 538 REMARK 465 ASN A 539 REMARK 465 THR A 540 REMARK 465 HIS A 541 REMARK 465 GLY A 542 REMARK 465 CYS A 543 REMARK 465 LYS A 544 REMARK 465 VAL A 545 REMARK 465 GLY A 546 REMARK 465 PRO A 547 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 ASN A 253 CB CG OD1 ND2 REMARK 470 LEU A 254 CG CD1 CD2 REMARK 470 HIS A 255 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 CG CD CE NZ REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 LYS A 287 CB CG CD CE NZ REMARK 470 SER A 288 OG REMARK 470 PHE A 289 CG CD1 CD2 CE1 CE2 CZ REMARK 470 HIS A 290 CB CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 291 CB CG CD CE NZ REMARK 470 VAL A 293 CB CG1 CG2 REMARK 470 SER A 295 OG REMARK 470 TYR A 296 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 297 CG CD OE1 NE2 REMARK 470 GLU A 298 CG CD OE1 OE2 REMARK 470 SER A 301 OG REMARK 470 ILE A 302 CD1 REMARK 470 ILE A 305 CD1 REMARK 470 LYS A 307 CG CD CE NZ REMARK 470 ARG A 308 CZ NH1 NH2 REMARK 470 ILE A 313 CD1 REMARK 470 ILE A 314 CG1 CG2 CD1 REMARK 470 ILE A 316 CD1 REMARK 470 GLU A 318 CG CD OE1 OE2 REMARK 470 SER A 319 OG REMARK 470 HIS A 321 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 322 CG CD1 CD2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 324 NZ REMARK 470 ILE A 328 CD1 REMARK 470 GLN A 397 CD OE1 NE2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 443 CG1 CG2 CD1 REMARK 470 ARG A 446 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 449 OD1 OD2 REMARK 470 VAL A 536 CG1 CG2 REMARK 470 LYS A 557 CD CE NZ REMARK 470 GLU A 572 CG CD OE1 OE2 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 -0.127 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. = -6.1 DEGREES REMARK 500 DG T 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA T 8 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 DA T 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DT T 10 O4' - C1' - N1 ANGL. DEV. = -5.0 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 288 -16.35 -141.77 REMARK 500 HIS A 290 -72.40 -44.19 REMARK 500 GLU A 318 -72.19 -58.59 REMARK 500 ASN A 407 114.37 -168.88 REMARK 500 CYS A 415 -136.64 -103.79 REMARK 500 ARG A 438 -33.98 -134.78 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 MN A 1 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ZAN A 0 O1B REMARK 620 2 ZAN A 0 O2G 88.5 REMARK 620 3 ZAN A 0 O1A 87.1 94.3 REMARK 620 4 HOH A 215 O 91.7 90.0 175.4 REMARK 620 5 ASP A 427 OD1 168.5 83.3 101.6 80.2 REMARK 620 6 ASP A 429 OD2 93.0 174.7 90.8 84.8 94.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 2 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ZAN A 0 O1A REMARK 620 2 HOH A 213 O 78.9 REMARK 620 3 ASP A 427 OD2 95.9 86.3 REMARK 620 4 ASP A 429 OD1 88.5 167.1 97.7 REMARK 620 5 ASP A 490 OD2 168.8 92.5 90.5 99.7 REMARK 620 6 DC P 6 O3' 95.6 86.2 164.8 92.5 76.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 3 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 195 O REMARK 620 2 HOH A 196 O 88.7 REMARK 620 3 HOH A 197 O 86.3 84.0 REMARK 620 4 HOH A 198 O 86.1 169.8 87.0 REMARK 620 5 ASP A 382 OD2 82.7 105.7 165.2 82.3 REMARK 620 6 HIS A 486 ND1 178.4 92.5 94.8 92.8 96.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 4 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 339 O REMARK 620 2 ILE A 341 O 91.6 REMARK 620 3 ALA A 344 O 80.5 80.8 REMARK 620 4 HOH A 578 O 88.6 102.9 168.6 REMARK 620 5 DA P 5 OP1 164.6 100.3 91.7 98.2 REMARK 620 6 HOH P 50 O 76.5 157.4 78.3 96.1 89.0 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 ZAN A 0 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 8 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MGH RELATED DB: PDB REMARK 900 RELATED ID: 3MGI RELATED DB: PDB REMARK 900 RELATED ID: 3UQ0 RELATED DB: PDB REMARK 900 RELATED ID: 3UQ1 RELATED DB: PDB REMARK 900 RELATED ID: 3UQ2 RELATED DB: PDB 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 3UPQ A 242 575 UNP Q9UGP5 DPOLL_HUMAN 242 575 DBREF 3UPQ T 1 11 PDB 3UPQ 3UPQ 1 11 DBREF 3UPQ P 1 6 PDB 3UPQ 3UPQ 1 6 DBREF 3UPQ D 1 4 PDB 3UPQ 3UPQ 1 4 SEQADV 3UPQ LYS A 463 UNP Q9UGP5 SER 463 SEE REMARK 999 SEQADV 3UPQ GLY A 464 UNP Q9UGP5 GLN 464 SEE REMARK 999 SEQADV 3UPQ GLU A 470 UNP Q9UGP5 GLN 470 SEE REMARK 999 SEQADV 3UPQ THR A 471 UNP Q9UGP5 GLN 471 SEE REMARK 999 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 CYS 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 DC SEQRES 1 D 4 DG DC DC DG HET ZAN A 0 31 HET MN A 1 1 HET MN A 2 1 HET MN A 3 1 HET NA A 4 1 HET SO4 A 5 5 HET SO4 A 6 5 HET SO4 A 7 5 HET SO4 A 8 5 HETNAM ZAN 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 ZAN PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION FORMUL 5 ZAN C10 H17 N6 O12 P3 FORMUL 6 MN 3(MN 2+) FORMUL 9 NA NA 1+ FORMUL 10 SO4 4(O4 S 2-) FORMUL 14 HOH *255(H2 O) HELIX 1 1 HIS A 255 GLN A 270 1 16 HELIX 2 2 ASP A 272 LYS A 287 1 16 HELIX 3 3 SER A 295 SER A 301 1 7 HELIX 4 4 GLY A 306 GLY A 320 1 15 HELIX 5 5 LEU A 322 ILE A 328 5 7 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 HIS A 379 GLU A 385 1 7 HELIX 11 11 ARG A 389 GLN A 404 1 16 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 PRO A 495 SER A 497 5 3 HELIX 15 15 GLU A 498 GLY A 508 1 11 HELIX 16 16 SER A 509 LYS A 523 1 15 HELIX 17 17 THR A 555 LEU A 563 1 9 HELIX 18 18 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 ASP A 427 THR A 433 -1 O LEU A 431 N VAL A 413 SHEET 3 B 5 ARG A 487 VAL A 493 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 VAL A 462 O LEU A 474 SHEET 1 C 3 MET A 525 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 VAL A 550 LEU A 551 -1 O LEU A 551 N LEU A 532 LINK O1B ZAN A 0 MN MN A 1 1555 1555 2.17 LINK O2G ZAN A 0 MN MN A 1 1555 1555 2.18 LINK O1A ZAN A 0 MN MN A 1 1555 1555 2.23 LINK O1A ZAN A 0 MN MN A 2 1555 1555 2.39 LINK MN MN A 1 O HOH A 215 1555 1555 2.29 LINK MN MN A 1 OD1 ASP A 427 1555 1555 2.09 LINK MN MN A 1 OD2 ASP A 429 1555 1555 2.17 LINK MN MN A 2 O HOH A 213 1555 1555 2.24 LINK MN MN A 2 OD2 ASP A 427 1555 1555 2.10 LINK MN MN A 2 OD1 ASP A 429 1555 1555 2.16 LINK MN MN A 2 OD2 ASP A 490 1555 1555 2.11 LINK MN MN A 2 O3' DC P 6 1555 1555 2.33 LINK MN MN A 3 O HOH A 195 1555 1555 2.21 LINK MN MN A 3 O HOH A 196 1555 1555 2.21 LINK MN MN A 3 O HOH A 197 1555 1555 2.18 LINK MN MN A 3 O HOH A 198 1555 1555 2.22 LINK MN MN A 3 OD2 ASP A 382 1555 1555 2.13 LINK MN MN A 3 ND1 HIS A 486 1555 1555 2.35 LINK NA NA A 4 O SER A 339 1555 1555 2.44 LINK NA NA A 4 O ILE A 341 1555 1555 2.62 LINK NA NA A 4 O ALA A 344 1555 1555 2.56 LINK NA NA A 4 O HOH A 578 1555 1555 2.41 LINK NA NA A 4 OP1 DA P 5 1555 1555 2.49 LINK NA NA A 4 O HOH P 50 1555 1555 2.60 CISPEP 1 GLY A 508 SER A 509 0 6.41 SITE 1 AC1 26 MN A 1 MN A 2 HOH A 52 HOH A 207 SITE 2 AC1 26 HOH A 208 HOH A 209 HOH A 211 HOH A 213 SITE 3 AC1 26 HOH A 223 ARG A 386 GLY A 416 SER A 417 SITE 4 AC1 26 ARG A 420 CYS A 425 GLY A 426 ASP A 427 SITE 5 AC1 26 ASP A 429 TYR A 505 PHE A 506 THR A 507 SITE 6 AC1 26 GLY A 508 ALA A 510 ASN A 513 DC P 6 SITE 7 AC1 26 HOH P 212 DT T 5 SITE 1 AC2 5 ZAN A 0 MN A 2 HOH A 215 ASP A 427 SITE 2 AC2 5 ASP A 429 SITE 1 AC3 7 ZAN A 0 MN A 1 HOH A 213 ASP A 427 SITE 2 AC3 7 ASP A 429 ASP A 490 DC P 6 SITE 1 AC4 6 HOH A 195 HOH A 196 HOH A 197 HOH A 198 SITE 2 AC4 6 ASP A 382 HIS A 486 SITE 1 AC5 6 SER A 339 ILE A 341 ALA A 344 HOH A 578 SITE 2 AC5 6 DA P 5 HOH P 50 SITE 1 AC6 5 HOH A 15 GLY A 442 ILE A 443 PHE A 444 SITE 2 AC6 5 SER A 445 SITE 1 AC7 3 HOH A 116 HIS A 440 ARG A 441 SITE 1 AC8 2 LYS A 273 TRP A 274 SITE 1 AC9 2 HOH A 104 ARG A 419 CRYST1 55.975 63.660 139.970 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 0.017865 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007144 0.00000