HEADER TRANSFERASE/TRANSFERASE INHIBITOR 20-OCT-10 3PB9 TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN GOLGI-RESIDENT TITLE 2 GLUTAMINYL CYCLASE IN COMPLEX WITH 1-BENZYLIMIDAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINYL-PEPTIDE CYCLOTRANSFERASE-LIKE PROTEIN; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: GOLGI-LUMINAL CATALYTIC DOMAIN; COMPND 5 SYNONYM: GOLGI-RESIDENT GLUTAMINYL CYCLASE; COMPND 6 EC: 2.3.2.5; 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: QPCTL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS ALPHA/BETA PROTEIN, ALPHA/BETA-MIXED FOLD, GLUTAMINYL CYCLASE, GOLGI KEYWDS 2 MEMBRANE, TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.F.HUANG,S.S.LIAW,W.L.HUANG,C.Y.CHIA,Y.C.LO,Y.L.CHEN,A.H.J.WANG REVDAT 3 01-NOV-23 3PB9 1 REMARK LINK REVDAT 2 03-AUG-11 3PB9 1 JRNL REVDAT 1 02-FEB-11 3PB9 0 JRNL AUTH K.F.HUANG,S.S.LIAW,W.L.HUANG,C.Y.CHIA,Y.C.LO,Y.L.CHEN, JRNL AUTH 2 A.H.J.WANG JRNL TITL STRUCTURES OF HUMAN GOLGI-RESIDENT GLUTAMINYL CYCLASE AND JRNL TITL 2 ITS COMPLEXES WITH INHIBITORS REVEAL A LARGE LOOP MOVEMENT JRNL TITL 3 UPON INHIBITOR BINDING JRNL REF J.BIOL.CHEM. V. 286 12439 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21288892 JRNL DOI 10.1074/JBC.M110.208595 REMARK 2 REMARK 2 RESOLUTION. 1.12 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.12 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 102035 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5393 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) : 1.12 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6921 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 351 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2444 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 463 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : -0.23000 REMARK 3 B33 (A**2) : -0.26000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.035 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.974 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2532 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3462 ; 2.268 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 308 ; 6.327 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;30.425 ;22.222 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 392 ;12.013 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;23.983 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 388 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1954 ; 0.015 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1558 ; 2.371 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2532 ; 3.308 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 974 ; 4.499 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 930 ; 6.158 ; 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): 2532 ; 2.664 ; 3.000 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 3PB9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 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 : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107676 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.120 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.12 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 3PB4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%(V/V) PEG 200, 5%(W/V) PEG 3000, REMARK 280 0.1M MES, PH 6.0, VAPOR DIFFUSION, SITTING 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 26.78100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.70100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.60100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.70100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.78100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.60100 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 SER X 53 REMARK 465 GLY X 54 REMARK 465 TRP X 55 REMARK 465 HIS X 56 REMARK 465 ARG X 57 REMARK 465 ARG X 58 REMARK 465 THR X 59 REMARK 465 GLU X 60 REMARK 465 GLU X 61 REMARK 465 LEU X 62 REMARK 465 PRO X 63 REMARK 465 LEU X 64 REMARK 465 GLY X 65 REMARK 465 ARG X 66 REMARK 465 GLU X 67 REMARK 465 LEU X 68 REMARK 465 ARG X 69 REMARK 465 VAL X 70 REMARK 465 PRO X 71 REMARK 465 LEU X 72 REMARK 465 ILE X 73 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 O HOH X 826 O HOH X 855 1.54 REMARK 500 O ALA X 79 O HOH X 849 1.59 REMARK 500 O HOH X 830 O HOH X 859 1.79 REMARK 500 CG2 THR X 179 O HOH X 839 1.81 REMARK 500 O HOH X 779 O HOH X 848 1.87 REMARK 500 O HOH X 842 O HOH X 852 1.94 REMARK 500 O HOH X 778 O HOH X 855 2.11 REMARK 500 CD ARG X 80 O HOH X 831 2.11 REMARK 500 NH1 ARG X 161 O HOH X 834 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH X 614 O HOH X 763 3654 1.76 REMARK 500 O HOH X 856 O HOH X 860 3544 1.79 REMARK 500 O HOH X 777 O HOH X 863 3554 2.02 REMARK 500 O HOH X 777 O HOH X 862 3554 2.03 REMARK 500 OE1 GLU X 230 O HOH X 851 3554 2.06 REMARK 500 REMARK 500 REMARK: NULL 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 SER X 125 CB SER X 125 OG 0.106 REMARK 500 GLU X 230 N GLU X 230 CA 0.145 REMARK 500 GLU X 230 CB GLU X 230 CG -0.198 REMARK 500 TRP X 231 CE2 TRP X 231 CZ2 0.114 REMARK 500 TRP X 231 CE3 TRP X 231 CZ3 0.189 REMARK 500 GLN X 245 CG GLN X 245 CD 0.169 REMARK 500 MET X 266 SD MET X 266 CE -0.431 REMARK 500 ARG X 291 CZ ARG X 291 NH2 0.086 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG X 124 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 THR X 127 OG1 - CB - CG2 ANGL. DEV. = 16.4 DEGREES REMARK 500 ASP X 147 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG X 158 CA - CB - CG ANGL. DEV. = 27.9 DEGREES REMARK 500 ARG X 161 CD - NE - CZ ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG X 161 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG X 161 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG X 207 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG X 207 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 LYS X 229 CA - C - N ANGL. DEV. = 13.6 DEGREES REMARK 500 GLU X 230 C - N - CA ANGL. DEV. = 16.7 DEGREES REMARK 500 MET X 266 CG - SD - CE ANGL. DEV. = -17.8 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 ARG X 105 49.90 -148.72 REMARK 500 LYS X 229 -0.06 -147.07 REMARK 500 GLU X 230 123.70 160.65 REMARK 500 ASP X 235 73.03 -112.26 REMARK 500 SER X 236 159.24 177.94 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 ZN X 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP X 186 OD2 REMARK 620 2 GLU X 226 OE2 107.2 REMARK 620 3 HIS X 351 NE2 98.6 114.6 REMARK 620 4 1BN X 390 N2 114.8 112.5 108.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1BN X 390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN X 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PB4 RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT PH 6.0 REMARK 900 RELATED ID: 3PB6 RELATED DB: PDB REMARK 900 RELATED ID: 3PB7 RELATED DB: PDB REMARK 900 RELATED ID: 3PB8 RELATED DB: PDB REMARK 900 RELATED ID: 3PBB RELATED DB: PDB REMARK 900 RELATED ID: 3PBE RELATED DB: PDB DBREF 3PB9 X 53 382 UNP Q9NXS2 QPCTL_HUMAN 53 382 SEQRES 1 X 330 SER GLY TRP HIS ARG ARG THR GLU GLU LEU PRO LEU GLY SEQRES 2 X 330 ARG GLU LEU ARG VAL PRO LEU ILE GLY SER LEU PRO GLU SEQRES 3 X 330 ALA ARG LEU ARG ARG VAL VAL GLY GLN LEU ASP PRO GLN SEQRES 4 X 330 ARG LEU TRP SER THR TYR LEU ARG PRO LEU LEU VAL VAL SEQRES 5 X 330 ARG THR PRO GLY SER PRO GLY ASN LEU GLN VAL ARG LYS SEQRES 6 X 330 PHE LEU GLU ALA THR LEU ARG SER LEU THR ALA GLY TRP SEQRES 7 X 330 HIS VAL GLU LEU ASP PRO PHE THR ALA SER THR PRO LEU SEQRES 8 X 330 GLY PRO VAL ASP PHE GLY ASN VAL VAL ALA THR LEU ASP SEQRES 9 X 330 PRO ARG ALA ALA ARG HIS LEU THR LEU ALA CYS HIS TYR SEQRES 10 X 330 ASP SER LYS LEU PHE PRO PRO GLY SER THR PRO PHE VAL SEQRES 11 X 330 GLY ALA THR ASP SER ALA VAL PRO CYS ALA LEU LEU LEU SEQRES 12 X 330 GLU LEU ALA GLN ALA LEU ASP LEU GLU LEU SER ARG ALA SEQRES 13 X 330 LYS LYS GLN ALA ALA PRO VAL THR LEU GLN LEU LEU PHE SEQRES 14 X 330 LEU ASP GLY GLU GLU ALA LEU LYS GLU TRP GLY PRO LYS SEQRES 15 X 330 ASP SER LEU TYR GLY SER ARG HIS LEU ALA GLN LEU MET SEQRES 16 X 330 GLU SER ILE PRO HIS SER PRO GLY PRO THR ARG ILE GLN SEQRES 17 X 330 ALA ILE GLU LEU PHE MET LEU LEU ASP LEU LEU GLY ALA SEQRES 18 X 330 PRO ASN PRO THR PHE TYR SER HIS PHE PRO ARG THR VAL SEQRES 19 X 330 ARG TRP PHE HIS ARG LEU ARG SER ILE GLU LYS ARG LEU SEQRES 20 X 330 HIS ARG LEU ASN LEU LEU GLN SER HIS PRO GLN GLU VAL SEQRES 21 X 330 MET TYR PHE GLN PRO GLY GLU PRO PHE GLY SER VAL GLU SEQRES 22 X 330 ASP ASP HIS ILE PRO PHE LEU ARG ARG GLY VAL PRO VAL SEQRES 23 X 330 LEU HIS LEU ILE SER THR PRO PHE PRO ALA VAL TRP HIS SEQRES 24 X 330 THR PRO ALA ASP THR GLU VAL ASN LEU HIS PRO PRO THR SEQRES 25 X 330 VAL HIS ASN LEU CYS ARG ILE LEU ALA VAL PHE LEU ALA SEQRES 26 X 330 GLU TYR LEU GLY LEU HET 1BN X 390 12 HET ZN X 400 1 HETNAM 1BN 1-BENZYL-1H-IMIDAZOLE HETNAM ZN ZINC ION HETSYN 1BN 1-BENZYLIMIDAZOLE FORMUL 2 1BN C10 H10 N2 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *463(H2 O) HELIX 1 1 PRO X 77 GLN X 87 1 11 HELIX 2 2 ASP X 89 TYR X 97 1 9 HELIX 3 3 LEU X 98 LEU X 102 5 5 HELIX 4 4 SER X 109 LEU X 126 1 18 HELIX 5 5 SER X 187 LEU X 201 1 15 HELIX 6 6 LEU X 201 GLN X 211 1 11 HELIX 7 7 LEU X 237 ILE X 250 1 14 HELIX 8 8 THR X 257 GLN X 260 5 4 HELIX 9 9 PHE X 282 ARG X 284 5 3 HELIX 10 10 THR X 285 LEU X 302 1 18 HELIX 11 11 HIS X 328 ARG X 333 1 6 HELIX 12 12 THR X 356 LEU X 360 5 5 HELIX 13 13 HIS X 361 GLY X 381 1 21 SHEET 1 A 6 HIS X 131 ALA X 139 0 SHEET 2 A 6 VAL X 146 THR X 154 -1 O PHE X 148 N PHE X 137 SHEET 3 A 6 VAL X 215 LEU X 222 -1 O LEU X 219 N ALA X 153 SHEET 4 A 6 ARG X 161 HIS X 168 1 N CYS X 167 O LEU X 222 SHEET 5 A 6 ILE X 262 ASP X 269 1 O MET X 266 N THR X 164 SHEET 6 A 6 VAL X 338 ILE X 342 1 O LEU X 339 N PHE X 265 LINK OD2 ASP X 186 ZN ZN X 400 1555 1555 1.99 LINK OE2 GLU X 226 ZN ZN X 400 1555 1555 1.95 LINK NE2 HIS X 351 ZN ZN X 400 1555 1555 2.00 LINK N2 1BN X 390 ZN ZN X 400 1555 1555 1.99 CISPEP 1 ASP X 186 SER X 187 0 5.57 CISPEP 2 SER X 253 PRO X 254 0 1.44 CISPEP 3 GLY X 255 PRO X 256 0 27.21 CISPEP 4 THR X 344 PRO X 345 0 6.22 SITE 1 AC1 9 ASP X 186 GLU X 225 GLU X 226 TRP X 231 SITE 2 AC1 9 ASP X 269 GLU X 325 TRP X 350 HIS X 351 SITE 3 AC1 9 ZN X 400 SITE 1 AC2 4 ASP X 186 GLU X 226 HIS X 351 1BN X 390 CRYST1 53.562 69.202 77.402 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 0.018670 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014450 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012920 0.00000