PDB Short entry for 3CTZ HEADER HYDROLASE 15-APR-08 3CTZ TITLE STRUCTURE OF HUMAN CYTOSOLIC X-PROLYL AMINOPEPTIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: XAA-PRO AMINOPEPTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: X-PRO AMINOPEPTIDASE 1, X-PROLYL AMINOPEPTIDASE 1, SOLUBLE, COMPND 5 CYTOSOLIC AMINOPEPTIDASE P, SOLUBLE AMINOPEPTIDASE P, SAMP, COMPND 6 AMINOACYLPROLINE AMINOPEPTIDASE; COMPND 7 EC: 3.4.11.9; COMPND 8 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: XPNPEP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PITA-BREAD FOLD, AMINOPEPTIDASE, HYDROLASE, MANGANESE, METAL-BINDING, KEYWDS 2 METALLOPROTEASE, PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR X.LI,Z.LOU,Z.RAO REVDAT 4 20-MAR-24 3CTZ 1 REMARK LINK REVDAT 3 29-JAN-14 3CTZ 1 JRNL VERSN REVDAT 2 24-FEB-09 3CTZ 1 VERSN REVDAT 1 27-MAY-08 3CTZ 0 JRNL AUTH X.LI,Z.LOU,X.LI,W.ZHOU,M.MA,Y.CAO,Y.GENG,M.BARTLAM, JRNL AUTH 2 X.C.ZHANG,Z.RAO JRNL TITL STRUCTURE OF HUMAN CYTOSOLIC X-PROLYL AMINOPEPTIDASE: A JRNL TITL 2 DOUBLE MN(II)-DEPENDENT DIMERIC ENZYME WITH A NOVEL JRNL TITL 3 THREE-DOMAIN SUBUNIT JRNL REF J.BIOL.CHEM. V. 283 22858 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18515364 JRNL DOI 10.1074/JBC.M710274200 REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 98520 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5155 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6943 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.1500 REMARK 3 BIN FREE R VALUE SET COUNT : 370 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4871 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 1055 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : -0.04000 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): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.079 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.758 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5128 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6989 ; 1.276 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 5.566 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;33.292 ;24.286 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 869 ;11.317 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.620 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 775 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3905 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2719 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3587 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 880 ; 0.190 ; 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): 50 ; 0.176 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 59 ; 0.186 ; 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): 3171 ; 1.169 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5163 ; 1.919 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2045 ; 2.839 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1825 ; 4.189 ; 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 3CTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 104753 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 0.15M CALCIUM CHLORIDE, REMARK 280 20% PEG 400, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.53800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 84.53800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.72200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.71450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.72200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.71450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 84.53800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.72200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.71450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 84.53800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.72200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.71450 REMARK 290 SMTRY3 8 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: 5400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 84.53800 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1211 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 SER A 620 REMARK 465 LYS A 621 REMARK 465 GLN A 622 REMARK 465 HIS A 623 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ASN A 553 REMARK 475 ARG A 554 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 PHE A 509 CB CG CD1 CD2 CE1 CE2 CZ 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 CE2 PHE A 509 O HOH A 1558 1.49 REMARK 500 O HOH A 659 O HOH A 1520 1.85 REMARK 500 O HOH A 891 O HOH A 1575 1.90 REMARK 500 O HOH A 1063 O HOH A 1650 1.92 REMARK 500 CZ PHE A 509 O HOH A 1558 1.93 REMARK 500 O HOH A 987 O HOH A 1640 1.99 REMARK 500 O HOH A 1519 O HOH A 1520 2.02 REMARK 500 O CYS A 308 O HOH A 1606 2.10 REMARK 500 O HOH A 1115 O HOH A 1584 2.13 REMARK 500 O HOH A 1267 O HOH A 1604 2.16 REMARK 500 O HOH A 1424 O HOH A 1544 2.17 REMARK 500 OD1 ASP A 469 O HOH A 1648 2.18 REMARK 500 O HOH A 1161 O HOH A 1470 2.19 REMARK 500 O HOH A 1144 O HOH A 1609 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 36 -169.24 -110.58 REMARK 500 GLU A 191 3.64 -69.09 REMARK 500 SER A 214 32.41 -150.01 REMARK 500 HIS A 218 -55.94 74.03 REMARK 500 HIS A 395 52.79 -101.54 REMARK 500 HIS A 395 56.48 -101.54 REMARK 500 ASP A 426 114.68 -165.45 REMARK 500 GLU A 434 -107.22 -152.38 REMARK 500 LEU A 484 54.65 -92.03 REMARK 500 ASP A 529 127.87 -39.98 REMARK 500 ALA A 531 -62.40 -130.55 REMARK 500 ASN A 553 -143.11 42.72 REMARK 500 ARG A 554 -49.30 97.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 553 10.91 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 625 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 415 OD1 REMARK 620 2 ASP A 415 OD2 57.9 REMARK 620 3 ASP A 426 OD1 98.1 154.9 REMARK 620 4 GLU A 537 OE1 94.2 98.6 89.7 REMARK 620 5 HOH A 644 O 144.8 87.4 117.1 84.7 REMARK 620 6 HOH A1518 O 100.7 88.0 90.0 164.9 82.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 624 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 426 OD2 REMARK 620 2 HIS A 489 NE2 85.3 REMARK 620 3 GLU A 523 OE2 142.2 85.7 REMARK 620 4 GLU A 537 OE2 77.8 124.6 77.5 REMARK 620 5 HOH A 644 O 111.5 155.9 90.2 77.3 REMARK 620 6 HOH A1519 O 85.5 88.8 130.8 140.4 76.0 REMARK 620 7 HOH A1520 O 131.0 79.3 82.8 147.1 76.6 48.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 626 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 435 O REMARK 620 2 THR A 435 OG1 71.0 REMARK 620 3 HOH A 670 O 80.7 71.4 REMARK 620 4 HOH A 717 O 111.8 141.7 71.6 REMARK 620 5 HOH A 739 O 142.7 75.7 73.0 84.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 627 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 507 NZ REMARK 620 2 HOH A 711 O 101.5 REMARK 620 3 HOH A1298 O 124.3 128.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 624 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 625 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 626 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 627 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P6G A 628 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR THINK THAT THESE ARE NATIVE MUTATION. DBREF 3CTZ A 1 623 UNP Q9NQW7 XPP1_HUMAN 1 623 SEQADV 3CTZ THR A 390 UNP Q9NQW7 ASN 390 SEE REMARK 999 SEQADV 3CTZ GLU A 434 UNP Q9NQW7 GLY 434 SEE REMARK 999 SEQADV 3CTZ LEU A 559 UNP Q9NQW7 PHE 559 SEE REMARK 999 SEQRES 1 A 623 MET PRO PRO LYS VAL THR SER GLU LEU LEU ARG GLN LEU SEQRES 2 A 623 ARG GLN ALA MET ARG ASN SER GLU TYR VAL THR GLU PRO SEQRES 3 A 623 ILE GLN ALA TYR ILE ILE PRO SER GLY ASP ALA HIS GLN SEQRES 4 A 623 SER GLU TYR ILE ALA PRO CYS ASP CYS ARG ARG ALA PHE SEQRES 5 A 623 VAL SER GLY PHE ASP GLY SER ALA GLY THR ALA ILE ILE SEQRES 6 A 623 THR GLU GLU HIS ALA ALA MET TRP THR ASP GLY ARG TYR SEQRES 7 A 623 PHE LEU GLN ALA ALA LYS GLN MET ASP SER ASN TRP THR SEQRES 8 A 623 LEU MET LYS MET GLY LEU LYS ASP THR PRO THR GLN GLU SEQRES 9 A 623 ASP TRP LEU VAL SER VAL LEU PRO GLU GLY SER ARG VAL SEQRES 10 A 623 GLY VAL ASP PRO LEU ILE ILE PRO THR ASP TYR TRP LYS SEQRES 11 A 623 LYS MET ALA LYS VAL LEU ARG SER ALA GLY HIS HIS LEU SEQRES 12 A 623 ILE PRO VAL LYS GLU ASN LEU VAL ASP LYS ILE TRP THR SEQRES 13 A 623 ASP ARG PRO GLU ARG PRO CYS LYS PRO LEU LEU THR LEU SEQRES 14 A 623 GLY LEU ASP TYR THR GLY ILE SER TRP LYS ASP LYS VAL SEQRES 15 A 623 ALA ASP LEU ARG LEU LYS MET ALA GLU ARG ASN VAL MET SEQRES 16 A 623 TRP PHE VAL VAL THR ALA LEU ASP GLU ILE ALA TRP LEU SEQRES 17 A 623 PHE ASN LEU ARG GLY SER ASP VAL GLU HIS ASN PRO VAL SEQRES 18 A 623 PHE PHE SER TYR ALA ILE ILE GLY LEU GLU THR ILE MET SEQRES 19 A 623 LEU PHE ILE ASP GLY ASP ARG ILE ASP ALA PRO SER VAL SEQRES 20 A 623 LYS GLU HIS LEU LEU LEU ASP LEU GLY LEU GLU ALA GLU SEQRES 21 A 623 TYR ARG ILE GLN VAL HIS PRO TYR LYS SER ILE LEU SER SEQRES 22 A 623 GLU LEU LYS ALA LEU CYS ALA ASP LEU SER PRO ARG GLU SEQRES 23 A 623 LYS VAL TRP VAL SER ASP LYS ALA SER TYR ALA VAL SER SEQRES 24 A 623 GLU THR ILE PRO LYS ASP HIS ARG CYS CYS MET PRO TYR SEQRES 25 A 623 THR PRO ILE CYS ILE ALA LYS ALA VAL LYS ASN SER ALA SEQRES 26 A 623 GLU SER GLU GLY MET ARG ARG ALA HIS ILE LYS ASP ALA SEQRES 27 A 623 VAL ALA LEU CYS GLU LEU PHE ASN TRP LEU GLU LYS GLU SEQRES 28 A 623 VAL PRO LYS GLY GLY VAL THR GLU ILE SER ALA ALA ASP SEQRES 29 A 623 LYS ALA GLU GLU PHE ARG ARG GLN GLN ALA ASP PHE VAL SEQRES 30 A 623 ASP LEU SER PHE PRO THR ILE SER SER THR GLY PRO THR SEQRES 31 A 623 GLY ALA ILE ILE HIS TYR ALA PRO VAL PRO GLU THR ASN SEQRES 32 A 623 ARG THR LEU SER LEU ASP GLU VAL TYR LEU ILE ASP SER SEQRES 33 A 623 GLY ALA GLN TYR LYS ASP GLY THR THR ASP VAL THR ARG SEQRES 34 A 623 THR MET HIS PHE GLU THR PRO THR ALA TYR GLU LYS GLU SEQRES 35 A 623 CYS PHE THR TYR VAL LEU LYS GLY HIS ILE ALA VAL SER SEQRES 36 A 623 ALA ALA VAL PHE PRO THR GLY THR LYS GLY HIS LEU LEU SEQRES 37 A 623 ASP SER PHE ALA ARG SER ALA LEU TRP ASP SER GLY LEU SEQRES 38 A 623 ASP TYR LEU HIS GLY THR GLY HIS GLY VAL GLY SER PHE SEQRES 39 A 623 LEU ASN VAL HIS GLU GLY PRO CYS GLY ILE SER TYR LYS SEQRES 40 A 623 THR PHE SER ASP GLU PRO LEU GLU ALA GLY MET ILE VAL SEQRES 41 A 623 THR ASP GLU PRO GLY TYR TYR GLU ASP GLY ALA PHE GLY SEQRES 42 A 623 ILE ARG ILE GLU ASN VAL VAL LEU VAL VAL PRO VAL LYS SEQRES 43 A 623 THR LYS TYR ASN PHE ASN ASN ARG GLY SER LEU THR LEU SEQRES 44 A 623 GLU PRO LEU THR LEU VAL PRO ILE GLN THR LYS MET ILE SEQRES 45 A 623 ASP VAL ASP SER LEU THR ASP LYS GLU CYS ASP TRP LEU SEQRES 46 A 623 ASN ASN TYR HIS LEU THR CYS ARG ASP VAL ILE GLY LYS SEQRES 47 A 623 GLU LEU GLN LYS GLN GLY ARG GLN GLU ALA LEU GLU TRP SEQRES 48 A 623 LEU ILE ARG GLU THR GLN PRO ILE SER LYS GLN HIS HET MN A 624 1 HET MN A 625 1 HET CA A 626 1 HET NA A 627 1 HET P6G A 628 19 HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM P6G HEXAETHYLENE GLYCOL HETSYN P6G POLYETHYLENE GLYCOL PEG400 FORMUL 2 MN 2(MN 2+) FORMUL 4 CA CA 2+ FORMUL 5 NA NA 1+ FORMUL 6 P6G C12 H26 O7 FORMUL 7 HOH *1055(H2 O) HELIX 1 1 THR A 6 MET A 17 1 12 HELIX 2 2 ALA A 44 ASP A 47 5 4 HELIX 3 3 CYS A 48 GLY A 55 1 8 HELIX 4 4 ASP A 75 ARG A 77 5 3 HELIX 5 5 TYR A 78 MET A 86 1 9 HELIX 6 6 THR A 102 LEU A 111 1 10 HELIX 7 7 PRO A 121 ILE A 124 5 4 HELIX 8 8 PRO A 125 ALA A 139 1 15 HELIX 9 9 ASN A 149 TRP A 155 1 7 HELIX 10 10 GLY A 170 GLY A 175 1 6 HELIX 11 11 SER A 177 GLU A 191 1 15 HELIX 12 12 ALA A 201 ASN A 210 1 10 HELIX 13 13 GLY A 239 ASP A 243 5 5 HELIX 14 14 ALA A 244 LEU A 251 1 8 HELIX 15 15 GLU A 258 TYR A 261 5 4 HELIX 16 16 PRO A 267 LYS A 269 5 3 HELIX 17 17 SER A 270 ASP A 281 1 12 HELIX 18 18 SER A 295 ILE A 302 1 8 HELIX 19 19 PRO A 303 ASP A 305 5 3 HELIX 20 20 THR A 313 VAL A 321 1 9 HELIX 21 21 ASN A 323 VAL A 352 1 30 HELIX 22 22 PRO A 353 GLY A 355 5 3 HELIX 23 23 THR A 358 GLN A 372 1 15 HELIX 24 24 PRO A 389 ILE A 393 5 5 HELIX 25 25 VAL A 399 ASN A 403 5 5 HELIX 26 26 THR A 437 ALA A 456 1 20 HELIX 27 27 LYS A 464 ALA A 472 5 9 HELIX 28 28 ARG A 473 SER A 479 1 7 HELIX 29 29 GLN A 568 ILE A 572 5 5 HELIX 30 30 ASP A 573 LEU A 577 5 5 HELIX 31 31 THR A 578 GLN A 603 1 26 HELIX 32 32 ARG A 605 GLU A 615 1 11 SHEET 1 A 6 TRP A 90 LYS A 94 0 SHEET 2 A 6 ALA A 70 THR A 74 1 N MET A 72 O MET A 93 SHEET 3 A 6 THR A 62 THR A 66 -1 N ILE A 64 O ALA A 71 SHEET 4 A 6 ALA A 29 ILE A 32 -1 N ILE A 32 O ALA A 63 SHEET 5 A 6 ARG A 116 VAL A 119 1 O GLY A 118 N ALA A 29 SHEET 6 A 6 HIS A 142 PRO A 145 1 O ILE A 144 N VAL A 117 SHEET 1 B 2 LEU A 167 THR A 168 0 SHEET 2 B 2 LEU A 211 ARG A 212 -1 O ARG A 212 N LEU A 167 SHEET 1 C 6 ILE A 263 HIS A 266 0 SHEET 2 C 6 ILE A 233 PHE A 236 1 N ILE A 233 O GLN A 264 SHEET 3 C 6 TYR A 225 GLY A 229 -1 N TYR A 225 O PHE A 236 SHEET 4 C 6 VAL A 194 VAL A 199 -1 N VAL A 199 O ALA A 226 SHEET 5 C 6 LYS A 287 SER A 291 1 O TRP A 289 N TRP A 196 SHEET 6 C 6 ARG A 307 MET A 310 1 O CYS A 308 N VAL A 288 SHEET 1 D 3 PHE A 376 LEU A 379 0 SHEET 2 D 3 ALA A 418 TYR A 420 -1 O GLN A 419 N ASP A 378 SHEET 3 D 3 GLY A 423 THR A 424 -1 O GLY A 423 N TYR A 420 SHEET 1 E 3 ILE A 384 THR A 387 0 SHEET 2 E 3 TYR A 412 SER A 416 -1 O LEU A 413 N SER A 386 SHEET 3 E 3 VAL A 427 MET A 431 -1 O MET A 431 N TYR A 412 SHEET 1 F 4 PHE A 459 PRO A 460 0 SHEET 2 F 4 SER A 556 PRO A 561 -1 O LEU A 557 N PHE A 459 SHEET 3 F 4 ASN A 538 VAL A 545 -1 N LEU A 541 O GLU A 560 SHEET 4 F 4 ILE A 519 ASP A 522 -1 N VAL A 520 O VAL A 540 SHEET 1 G 2 GLY A 488 HIS A 489 0 SHEET 2 G 2 GLY A 503 ILE A 504 -1 O ILE A 504 N GLY A 488 SHEET 1 H 2 GLY A 525 GLU A 528 0 SHEET 2 H 2 PHE A 532 ARG A 535 -1 O PHE A 532 N GLU A 528 LINK OD1 ASP A 415 MN MN A 625 1555 1555 2.15 LINK OD2 ASP A 415 MN MN A 625 1555 1555 2.34 LINK OD2 ASP A 426 MN MN A 624 1555 1555 2.38 LINK OD1 ASP A 426 MN MN A 625 1555 1555 2.14 LINK O THR A 435 CA CA A 626 1555 1555 2.43 LINK OG1 THR A 435 CA CA A 626 1555 1555 2.56 LINK NE2 HIS A 489 MN MN A 624 1555 1555 2.27 LINK NZ LYS A 507 NA NA A 627 1555 1555 2.91 LINK OE2 GLU A 523 MN MN A 624 1555 1555 2.27 LINK OE2 GLU A 537 MN MN A 624 1555 1555 2.26 LINK OE1 GLU A 537 MN MN A 625 1555 1555 2.18 LINK MN MN A 624 O HOH A 644 1555 1555 2.30 LINK MN MN A 624 O HOH A1519 1555 1555 2.17 LINK MN MN A 624 O HOH A1520 1555 1555 2.66 LINK MN MN A 625 O HOH A 644 1555 1555 2.23 LINK MN MN A 625 O HOH A1518 1555 1555 2.27 LINK CA CA A 626 O HOH A 670 1555 1555 2.49 LINK CA CA A 626 O HOH A 717 1555 1555 2.48 LINK CA CA A 626 O HOH A 739 1555 1555 2.48 LINK NA NA A 627 O HOH A 711 1555 1555 3.14 LINK NA NA A 627 O HOH A1298 1555 1555 3.16 CISPEP 1 GLY A 500 PRO A 501 0 -1.18 SITE 1 AC1 7 ASP A 426 HIS A 489 GLU A 523 GLU A 537 SITE 2 AC1 7 HOH A 644 HOH A1519 HOH A1520 SITE 1 AC2 7 PHE A 381 ASP A 415 ASP A 426 THR A 428 SITE 2 AC2 7 GLU A 537 HOH A 644 HOH A1518 SITE 1 AC3 7 ASP A 281 THR A 435 HOH A 658 HOH A 670 SITE 2 AC3 7 HOH A 717 HOH A 739 HOH A 752 SITE 1 AC4 2 GLY A 486 LYS A 507 SITE 1 AC5 14 PHE A 381 ILE A 394 HIS A 395 HIS A 485 SITE 2 AC5 14 GLY A 486 HIS A 489 HIS A 498 GLU A 523 SITE 3 AC5 14 HOH A 659 HOH A 792 HOH A 861 HOH A1298 SITE 4 AC5 14 HOH A1518 HOH A1520 CRYST1 71.444 131.429 169.076 90.00 90.00 90.00 C 2 2 21 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 0.013997 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005914 0.00000