PDB Short entry for 2ZEJ HEADER TRANSFERASE 13-DEC-07 2ZEJ TITLE STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S DISEASE-ASSOCIATED TITLE 2 LEUCINE-RICH REPEAT KINASE 2 REVEALS A DIMERIC GTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-RICH REPEAT KINASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ROC-GTPASE DOMAIN, UNP RESIDUES 1333-1516; COMPND 5 SYNONYM: DARDARIN; COMPND 6 EC: 2.7.11.1; COMPND 7 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: LRRK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21GOLDDE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSKB3 KEYWDS PARKINSON'S DISEASE, LRRK2, ROC, GTPASE, ROCO, KINASE, ATP-BINDING, KEYWDS 2 DISEASE MUTATION, GTP-BINDING, GTPASE ACTIVATION, LEUCINE-RICH KEYWDS 3 REPEAT, MEMBRANE, NUCLEOTIDE-BINDING, PARKINSON DISEASE, KEYWDS 4 SERINE/THREONINE-PROTEIN KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.DENG REVDAT 6 11-OCT-17 2ZEJ 1 REMARK REVDAT 5 13-JUL-11 2ZEJ 1 VERSN REVDAT 4 24-FEB-09 2ZEJ 1 VERSN REVDAT 3 22-APR-08 2ZEJ 1 JRNL REVDAT 2 12-FEB-08 2ZEJ 1 JRNL REVDAT 1 22-JAN-08 2ZEJ 0 JRNL AUTH J.DENG,P.A.LEWIS,E.GREGGIO,E.SLUCH,A.BEILINA,M.R.COOKSON JRNL TITL STRUCTURE OF THE ROC DOMAIN FROM THE PARKINSON'S JRNL TITL 2 DISEASE-ASSOCIATED LEUCINE-RICH REPEAT KINASE 2 REVEALS A JRNL TITL 3 DIMERIC GTPASE JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 1499 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18230735 JRNL DOI 10.1073/PNAS.0709098105 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0037 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 NUMBER OF REFLECTIONS : 22346 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1191 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2538 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 29.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : 0.76000 REMARK 3 B12 (A**2) : -0.16000 REMARK 3 B13 (A**2) : -0.43000 REMARK 3 B23 (A**2) : -0.38000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.198 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.660 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2601 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3530 ; 2.145 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 317 ;15.908 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;34.987 ;24.571 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 455 ;20.045 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;20.346 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 408 ; 0.270 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1876 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1097 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1725 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 165 ; 0.139 ; 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): 33 ; 0.202 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.222 ; 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): 1634 ; 1.206 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2556 ; 1.736 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1127 ; 3.497 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 972 ; 4.627 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1335 A 1507 REMARK 3 ORIGIN FOR THE GROUP (A): 29.4030 37.2140 44.7930 REMARK 3 T TENSOR REMARK 3 T11: -0.1422 T22: -0.0961 REMARK 3 T33: 0.0565 T12: 0.0392 REMARK 3 T13: -0.0209 T23: -0.0677 REMARK 3 L TENSOR REMARK 3 L11: 2.2397 L22: 1.6663 REMARK 3 L33: 0.8813 L12: 0.9937 REMARK 3 L13: -0.6975 L23: -0.2484 REMARK 3 S TENSOR REMARK 3 S11: -0.0109 S12: -0.2056 S13: -0.2176 REMARK 3 S21: 0.0711 S22: -0.0122 S23: -0.0512 REMARK 3 S31: 0.1104 S32: -0.0294 S33: 0.0231 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1336 B 1510 REMARK 3 ORIGIN FOR THE GROUP (A): 44.6750 49.9640 33.2210 REMARK 3 T TENSOR REMARK 3 T11: -0.1452 T22: -0.1007 REMARK 3 T33: 0.0367 T12: 0.0347 REMARK 3 T13: -0.0028 T23: -0.0865 REMARK 3 L TENSOR REMARK 3 L11: 2.3402 L22: 1.9717 REMARK 3 L33: 0.8358 L12: 0.8869 REMARK 3 L13: -0.7825 L23: -0.5634 REMARK 3 S TENSOR REMARK 3 S11: 0.0136 S12: -0.0048 S13: 0.0275 REMARK 3 S21: -0.1842 S22: -0.0553 S23: -0.1414 REMARK 3 S31: -0.0609 S32: 0.0771 S33: 0.0416 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2ZEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000027871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97948 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23675 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.9000 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) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 100MM MGCL2, 0.1M TRIS, REMARK 280 5MM GTP, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 7850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASN A 1333 REMARK 465 ARG A 1334 REMARK 465 THR A 1357 REMARK 465 LYS A 1358 REMARK 465 LYS A 1359 REMARK 465 SER A 1360 REMARK 465 ASP A 1361 REMARK 465 LEU A 1362 REMARK 465 GLY A 1363 REMARK 465 MSE A 1364 REMARK 465 GLN A 1365 REMARK 465 SER A 1366 REMARK 465 ALA A 1367 REMARK 465 GLN A 1379 REMARK 465 ILE A 1380 REMARK 465 ARG A 1381 REMARK 465 ASP A 1382 REMARK 465 LYS A 1383 REMARK 465 ARG A 1384 REMARK 465 LYS A 1385 REMARK 465 ARG A 1386 REMARK 465 ASP A 1387 REMARK 465 LYS A 1512 REMARK 465 ILE A 1513 REMARK 465 ARG A 1514 REMARK 465 ASP A 1515 REMARK 465 GLN A 1516 REMARK 465 ASN B 1333 REMARK 465 ARG B 1334 REMARK 465 LYS B 1358 REMARK 465 LYS B 1359 REMARK 465 SER B 1360 REMARK 465 ASP B 1361 REMARK 465 LEU B 1362 REMARK 465 GLY B 1363 REMARK 465 MSE B 1364 REMARK 465 GLN B 1379 REMARK 465 ILE B 1380 REMARK 465 ARG B 1381 REMARK 465 ASP B 1382 REMARK 465 LYS B 1383 REMARK 465 ARG B 1384 REMARK 465 LYS B 1385 REMARK 465 ARG B 1386 REMARK 465 ASP B 1387 REMARK 465 ILE B 1513 REMARK 465 ARG B 1514 REMARK 465 ASP B 1515 REMARK 465 GLN B 1516 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 1356 CE NZ REMARK 480 ARG A 1398 CG REMARK 480 GLN A 1411 CB CG REMARK 480 ARG A 1412 CD NE REMARK 480 LYS A 1463 CG CD CE NZ REMARK 480 LYS A 1471 CD CE NZ REMARK 480 ARG A 1477 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 1483 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 1493 CG CD OE1 OE2 REMARK 480 LYS A 1499 CE NZ REMARK 480 PHE A 1511 CG CD1 CD2 CE1 CE2 CZ REMARK 480 LYS B 1356 CE NZ REMARK 480 GLN B 1365 CG CD OE1 NE2 REMARK 480 SER B 1366 CB OG REMARK 480 LYS B 1439 CE NZ REMARK 480 LYS B 1463 NZ REMARK 480 LYS B 1471 CD CE NZ REMARK 480 ARG B 1477 CB CG CD NE CZ NH1 NH2 REMARK 480 TYR B 1485 CE1 OH REMARK 480 LYS B 1512 CG CD CE NZ 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 ARG A1412 47.74 -103.68 REMARK 500 ASN A1510 68.55 -108.90 REMARK 500 ARG B1462 -37.90 -139.48 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 GLN B 1461 ARG B 1462 -127.62 REMARK 500 ARG B 1462 LYS B 1463 135.33 REMARK 500 ARG B 1477 GLY B 1478 -58.91 REMARK 500 GLY B 1478 PHE B 1479 144.16 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 MG A 2 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A1348 OG1 REMARK 620 2 GDP A 1 O3B 93.0 REMARK 620 3 HOH A 201 O 84.7 90.1 REMARK 620 4 HOH A 104 O 97.4 85.8 175.4 REMARK 620 5 HOH A 200 O 172.6 92.5 90.5 87.9 REMARK 620 6 HOH A 202 O 91.0 176.0 90.3 93.7 83.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B1348 OG1 REMARK 620 2 GDP B 2 O3B 92.3 REMARK 620 3 HOH B1519 O 171.7 95.5 REMARK 620 4 HOH B1517 O 85.5 170.6 86.4 REMARK 620 5 HOH B1518 O 88.7 95.0 93.3 94.1 REMARK 620 6 HOH B1569 O 86.8 89.5 90.5 81.2 173.7 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 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 2 DBREF 2ZEJ A 1333 1516 UNP Q17RV3 Q17RV3_HUMAN 1333 1516 DBREF 2ZEJ B 1333 1516 UNP Q17RV3 Q17RV3_HUMAN 1333 1516 SEQRES 1 A 184 ASN ARG MSE LYS LEU MSE ILE VAL GLY ASN THR GLY SER SEQRES 2 A 184 GLY LYS THR THR LEU LEU GLN GLN LEU MSE LYS THR LYS SEQRES 3 A 184 LYS SER ASP LEU GLY MSE GLN SER ALA THR VAL GLY ILE SEQRES 4 A 184 ASP VAL LYS ASP TRP PRO ILE GLN ILE ARG ASP LYS ARG SEQRES 5 A 184 LYS ARG ASP LEU VAL LEU ASN VAL TRP ASP PHE ALA GLY SEQRES 6 A 184 ARG GLU GLU PHE TYR SER THR HIS PRO HIS PHE MSE THR SEQRES 7 A 184 GLN ARG ALA LEU TYR LEU ALA VAL TYR ASP LEU SER LYS SEQRES 8 A 184 GLY GLN ALA GLU VAL ASP ALA MSE LYS PRO TRP LEU PHE SEQRES 9 A 184 ASN ILE LYS ALA ARG ALA SER SER SER PRO VAL ILE LEU SEQRES 10 A 184 VAL GLY THR HIS LEU ASP VAL SER ASP GLU LYS GLN ARG SEQRES 11 A 184 LYS ALA CYS MSE SER LYS ILE THR LYS GLU LEU LEU ASN SEQRES 12 A 184 LYS ARG GLY PHE PRO ALA ILE ARG ASP TYR HIS PHE VAL SEQRES 13 A 184 ASN ALA THR GLU GLU SER ASP ALA LEU ALA LYS LEU ARG SEQRES 14 A 184 LYS THR ILE ILE ASN GLU SER LEU ASN PHE LYS ILE ARG SEQRES 15 A 184 ASP GLN SEQRES 1 B 184 ASN ARG MSE LYS LEU MSE ILE VAL GLY ASN THR GLY SER SEQRES 2 B 184 GLY LYS THR THR LEU LEU GLN GLN LEU MSE LYS THR LYS SEQRES 3 B 184 LYS SER ASP LEU GLY MSE GLN SER ALA THR VAL GLY ILE SEQRES 4 B 184 ASP VAL LYS ASP TRP PRO ILE GLN ILE ARG ASP LYS ARG SEQRES 5 B 184 LYS ARG ASP LEU VAL LEU ASN VAL TRP ASP PHE ALA GLY SEQRES 6 B 184 ARG GLU GLU PHE TYR SER THR HIS PRO HIS PHE MSE THR SEQRES 7 B 184 GLN ARG ALA LEU TYR LEU ALA VAL TYR ASP LEU SER LYS SEQRES 8 B 184 GLY GLN ALA GLU VAL ASP ALA MSE LYS PRO TRP LEU PHE SEQRES 9 B 184 ASN ILE LYS ALA ARG ALA SER SER SER PRO VAL ILE LEU SEQRES 10 B 184 VAL GLY THR HIS LEU ASP VAL SER ASP GLU LYS GLN ARG SEQRES 11 B 184 LYS ALA CYS MSE SER LYS ILE THR LYS GLU LEU LEU ASN SEQRES 12 B 184 LYS ARG GLY PHE PRO ALA ILE ARG ASP TYR HIS PHE VAL SEQRES 13 B 184 ASN ALA THR GLU GLU SER ASP ALA LEU ALA LYS LEU ARG SEQRES 14 B 184 LYS THR ILE ILE ASN GLU SER LEU ASN PHE LYS ILE ARG SEQRES 15 B 184 ASP GLN MODRES 2ZEJ MSE A 1335 MET SELENOMETHIONINE MODRES 2ZEJ MSE A 1338 MET SELENOMETHIONINE MODRES 2ZEJ MSE A 1355 MET SELENOMETHIONINE MODRES 2ZEJ MSE A 1409 MET SELENOMETHIONINE MODRES 2ZEJ MSE A 1431 MET SELENOMETHIONINE MODRES 2ZEJ MSE A 1466 MET SELENOMETHIONINE MODRES 2ZEJ MSE B 1335 MET SELENOMETHIONINE MODRES 2ZEJ MSE B 1338 MET SELENOMETHIONINE MODRES 2ZEJ MSE B 1355 MET SELENOMETHIONINE MODRES 2ZEJ MSE B 1409 MET SELENOMETHIONINE MODRES 2ZEJ MSE B 1431 MET SELENOMETHIONINE MODRES 2ZEJ MSE B 1466 MET SELENOMETHIONINE HET MSE A1335 8 HET MSE A1338 8 HET MSE A1355 8 HET MSE A1409 8 HET MSE A1431 8 HET MSE A1466 8 HET MSE B1335 8 HET MSE B1338 8 HET MSE B1355 8 HET MSE B1409 8 HET MSE B1431 8 HET MSE B1466 8 HET MG A 2 1 HET GDP A 1 28 HET MG B 1 1 HET GDP B 2 28 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 3 MG 2(MG 2+) FORMUL 4 GDP 2(C10 H15 N5 O11 P2) FORMUL 7 HOH *112(H2 O) HELIX 1 1 GLY A 1346 LYS A 1356 1 11 HELIX 2 2 GLY A 1397 SER A 1403 1 7 HELIX 3 3 HIS A 1405 ARG A 1412 1 8 HELIX 4 4 GLY A 1424 ALA A 1430 1 7 HELIX 5 5 ALA A 1430 ALA A 1442 1 13 HELIX 6 6 HIS A 1453 SER A 1457 5 5 HELIX 7 7 ASP A 1458 LEU A 1473 1 16 HELIX 8 8 SER A 1494 ASN A 1510 1 17 HELIX 9 9 GLY B 1346 LYS B 1356 1 11 HELIX 10 10 GLY B 1397 THR B 1404 1 8 HELIX 11 11 HIS B 1405 ARG B 1412 1 8 HELIX 12 12 GLY B 1424 ALA B 1430 1 7 HELIX 13 13 ALA B 1430 ALA B 1442 1 13 HELIX 14 14 HIS B 1453 ASP B 1458 5 6 HELIX 15 15 GLU B 1459 LEU B 1473 1 15 HELIX 16 16 SER B 1494 LYS B 1512 1 19 SHEET 1 A 6 ILE A1371 TRP A1376 0 SHEET 2 A 6 LEU A1390 PHE A1395 -1 O VAL A1392 N LYS A1374 SHEET 3 A 6 LYS A1336 VAL A1340 1 N LEU A1337 O TRP A1393 SHEET 4 A 6 ALA B1413 ASP B1420 1 O LEU B1414 N MSE A1338 SHEET 5 A 6 PRO B1446 THR B1452 1 O VAL B1450 N ALA B1417 SHEET 6 A 6 ALA B1481 PHE B1487 1 O ALA B1481 N VAL B1447 SHEET 1 B 6 ALA A1481 PHE A1487 0 SHEET 2 B 6 PRO A1446 THR A1452 1 N VAL A1447 O ARG A1483 SHEET 3 B 6 ALA A1413 ASP A1420 1 N ALA A1417 O VAL A1450 SHEET 4 B 6 LYS B1336 GLY B1341 1 O MSE B1338 N LEU A1414 SHEET 5 B 6 LEU B1390 PHE B1395 1 O TRP B1393 N LEU B1337 SHEET 6 B 6 ILE B1371 TRP B1376 -1 N LYS B1374 O VAL B1392 LINK OG1 THR A1348 MG MG A 2 1555 1555 2.09 LINK OG1 THR B1348 MG MG B 1 1555 1555 2.12 LINK MG MG B 1 O3B GDP B 2 1555 1555 2.09 LINK MG MG A 2 O3B GDP A 1 1555 1555 2.02 LINK MG MG A 2 O HOH A 201 1555 1555 2.24 LINK MG MG A 2 O HOH A 104 1555 1555 2.19 LINK MG MG A 2 O HOH A 200 1555 1555 2.05 LINK MG MG A 2 O HOH A 202 1555 1555 2.14 LINK MG MG B 1 O HOH B1519 1555 1555 2.03 LINK MG MG B 1 O HOH B1517 1555 1555 2.16 LINK MG MG B 1 O HOH B1518 1555 1555 2.17 LINK MG MG B 1 O HOH B1569 1555 1555 2.31 LINK C MSE A1335 N LYS A1336 1555 1555 1.34 LINK C LEU A1337 N MSE A1338 1555 1555 1.33 LINK C MSE A1338 N ILE A1339 1555 1555 1.34 LINK C LEU A1354 N MSE A1355 1555 1555 1.31 LINK C MSE A1355 N LYS A1356 1555 1555 1.32 LINK C PHE A1408 N MSE A1409 1555 1555 1.33 LINK C MSE A1409 N THR A1410 1555 1555 1.33 LINK C ALA A1430 N MSE A1431 1555 1555 1.33 LINK C MSE A1431 N LYS A1432 1555 1555 1.34 LINK C CYS A1465 N MSE A1466 1555 1555 1.33 LINK C MSE A1466 N SER A1467 1555 1555 1.34 LINK C MSE B1335 N LYS B1336 1555 1555 1.33 LINK C LEU B1337 N MSE B1338 1555 1555 1.32 LINK C MSE B1338 N ILE B1339 1555 1555 1.34 LINK C LEU B1354 N MSE B1355 1555 1555 1.33 LINK C MSE B1355 N LYS B1356 1555 1555 1.34 LINK C PHE B1408 N MSE B1409 1555 1555 1.33 LINK C MSE B1409 N THR B1410 1555 1555 1.32 LINK C ALA B1430 N MSE B1431 1555 1555 1.32 LINK C MSE B1431 N LYS B1432 1555 1555 1.33 LINK C CYS B1465 N MSE B1466 1555 1555 1.33 LINK C MSE B1466 N SER B1467 1555 1555 1.34 CISPEP 1 ARG A 1477 GLY A 1478 0 -15.45 SITE 1 AC1 6 GDP A 1 HOH A 104 HOH A 200 HOH A 201 SITE 2 AC1 6 HOH A 202 THR A1348 SITE 1 AC2 6 GDP B 2 THR B1348 HOH B1517 HOH B1518 SITE 2 AC2 6 HOH B1519 HOH B1569 SITE 1 AC3 22 MG A 2 HOH A 10 HOH A 22 HOH A 49 SITE 2 AC3 22 HOH A 104 HOH A 114 HOH A 116 HOH A 200 SITE 3 AC3 22 HOH A 201 GLY A1344 SER A1345 GLY A1346 SITE 4 AC3 22 LYS A1347 THR A1348 THR A1349 PHE A1436 SITE 5 AC3 22 ASN A1437 HIS B1453 ASP B1455 ASN B1489 SITE 6 AC3 22 ALA B1490 THR B1491 SITE 1 AC4 21 HIS A1453 ASP A1455 ASN A1489 ALA A1490 SITE 2 AC4 21 THR A1491 MG B 1 THR B1343 GLY B1344 SITE 3 AC4 21 SER B1345 GLY B1346 LYS B1347 THR B1348 SITE 4 AC4 21 THR B1349 PHE B1436 ASN B1437 HOH B1519 SITE 5 AC4 21 HOH B1522 HOH B1527 HOH B1538 HOH B1556 SITE 6 AC4 21 HOH B1569 CRYST1 44.438 44.404 53.681 81.51 69.00 78.71 P 1 2 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 0.022503 -0.004493 -0.008288 0.00000 SCALE2 0.000000 0.022965 -0.001950 0.00000 SCALE3 0.000000 0.000000 0.020026 0.00000 HETATM 1 N MSE A1335 40.849 41.003 24.904 1.00 38.86 N HETATM 2 CA MSE A1335 39.557 41.091 25.644 1.00 39.43 C HETATM 3 C MSE A1335 39.530 42.116 26.793 1.00 37.45 C HETATM 4 O MSE A1335 38.606 42.922 26.814 1.00 36.14 O HETATM 5 CB MSE A1335 39.095 39.709 26.133 1.00 41.32 C HETATM 6 CG MSE A1335 37.758 39.625 26.797 1.00 48.96 C HETATM 7 SE MSE A1335 36.341 39.046 25.517 1.00 76.92 SE HETATM 8 CE MSE A1335 37.131 37.319 24.900 1.00 67.30 C