HEADER HYDROLASE 28-NOV-08 3FED TITLE THE HIGH RESOLUTION STRUCTURE OF HUMAN GLUTAMATE CARBOXYPEPTIDASE III TITLE 2 (GCPIII/NAALADASE II) IN COMPLEX WITH A TRANSITION STATE ANALOG OF TITLE 3 GLU-GLU COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE CARBOXYPEPTIDASE III; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 5 SYNONYM: GCPIII, N-ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE 2, N- COMPND 6 ACETYLATED-ALPHA-LINKED ACIDIC DIPEPTIDASE II, NAALADASE II; COMPND 7 EC: 3.4.17.21; 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: NAALAD2; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SCHNEIDER'S S2 CELLS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS METALLOPEPTIDASE, BIMETALLIC ACTIVE SITE, N-GLYCOSYLATION, CALCIUM KEYWDS 2 CATION, CHLORIDE ANION, ZINC IONS, CARBOXYPEPTIDASE, DIPEPTIDASE, KEYWDS 3 GLYCOPROTEIN, HYDROLASE, MEMBRANE, METAL-BINDING, METALLOPROTEASE, KEYWDS 4 MULTIFUNCTIONAL ENZYME, PROTEASE, SIGNAL-ANCHOR, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR J.LUBKOWSKI,C.BARINKA,K.HLOUCHOVA REVDAT 4 06-SEP-23 3FED 1 HETSYN REVDAT 3 29-JUL-20 3FED 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 13-JUL-11 3FED 1 VERSN REVDAT 1 25-AUG-09 3FED 0 JRNL AUTH K.HLOUCHOVA,C.BARINKA,J.KONVALINKA,J.LUBKOWSKI JRNL TITL STRUCTURAL INSIGHT INTO THE EVOLUTIONARY AND PHARMACOLOGIC JRNL TITL 2 HOMOLOGY OF GLUTAMATE CARBOXYPEPTIDASES II AND III JRNL REF FEBS J. V. 276 4448 2009 JRNL REFN ISSN 1742-464X JRNL PMID 19678840 JRNL DOI 10.1111/J.1742-4658.2009.07152.X REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0057 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 225644 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) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2292 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) : 1.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 14444 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5504 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 861 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.25000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.954 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6093 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8293 ; 1.830 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 741 ; 5.860 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 282 ;35.741 ;24.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1091 ;13.484 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;18.777 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 916 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4612 ; 0.014 ; 0.021 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): 3592 ; 1.862 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5880 ; 2.701 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2501 ; 3.568 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2392 ; 5.186 ; 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): 6093 ; 2.058 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 865 ; 9.960 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5919 ; 5.474 ; 3.000 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 : 1 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 46 A 1760 REMARK 3 ORIGIN FOR THE GROUP (A): 19.3540 45.7880 13.3900 REMARK 3 T TENSOR REMARK 3 T11: -0.0205 T22: -0.0083 REMARK 3 T33: -0.0085 T12: 0.0054 REMARK 3 T13: -0.0006 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.1285 L22: 0.2001 REMARK 3 L33: 0.2067 L12: -0.0700 REMARK 3 L13: 0.0387 L23: -0.1258 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: -0.0213 S13: 0.0134 REMARK 3 S21: 0.0151 S22: 0.0100 S23: -0.0218 REMARK 3 S31: -0.0035 S32: 0.0497 S33: 0.0012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 3FED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-06 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-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 227958 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 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 (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: COOT REMARK 200 STARTING MODEL: PDB ENTRY 2OR4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NA, 10% (W/V) PEG6000, 5% REMARK 280 (V/V) MPD, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 61.36550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.04300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 61.36550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 52.04300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 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 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 0.00000 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 A 7 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1054 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1434 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 ARG A 34 REMARK 465 SER A 35 REMARK 465 GLU A 36 REMARK 465 THR A 37 REMARK 465 THR A 38 REMARK 465 THR A 39 REMARK 465 SER A 40 REMARK 465 VAL A 41 REMARK 465 ARG A 42 REMARK 465 TYR A 43 REMARK 465 HIS A 44 REMARK 465 GLN A 45 REMARK 465 TYR A 133 REMARK 465 LEU A 134 REMARK 465 GLU A 135 REMARK 465 ASP A 327 REMARK 465 LEU A 740 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 NH1 ARG A 639 O HOH A 983 1.41 REMARK 500 ND2 ASN A 185 O5 NAG A 1757 1.57 REMARK 500 ND2 ASN A 250 O HOH A 1090 1.88 REMARK 500 OE1 GLU A 266 O HOH A 1100 1.92 REMARK 500 OE2 GLU A 293 O HOH A 1164 1.96 REMARK 500 O HOH A 804 O HOH A 981 1.98 REMARK 500 O HOH A 886 O HOH A 1241 2.04 REMARK 500 O HOH A 888 O HOH A 1344 2.05 REMARK 500 O HOH A 1317 O HOH A 1406 2.08 REMARK 500 O HOH A 1218 O HOH A 1335 2.12 REMARK 500 OD2 ASP A 534 O HOH A 884 2.12 REMARK 500 O4 NAG A 1756 O HOH A 853 2.13 REMARK 500 O HOH A 814 O HOH A 950 2.14 REMARK 500 NE ARG A 639 O HOH A 1417 2.14 REMARK 500 O HOH A 803 O HOH A 981 2.15 REMARK 500 O HOH A 978 O HOH A 1223 2.17 REMARK 500 O HOH A 823 O HOH A 870 2.17 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 A 885 O HOH A 1243 2555 1.93 REMARK 500 O HOH A 993 O HOH A 1190 2555 2.08 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 GLU A 173 CD GLU A 173 OE1 0.067 REMARK 500 ARG A 270 CG ARG A 270 CD -0.160 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 A 48 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 194 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 455 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 MET A 654 CB - CG - SD ANGL. DEV. = -18.7 DEGREES REMARK 500 ARG A 663 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ALA A 98 102.22 -160.53 REMARK 500 PHE A 154 4.35 81.74 REMARK 500 ASN A 168 -129.15 59.66 REMARK 500 LYS A 197 -45.31 74.78 REMARK 500 VAL A 372 -113.03 -130.24 REMARK 500 SER A 442 56.63 -143.27 REMARK 500 ASP A 443 -158.65 -83.92 REMARK 500 ASN A 496 107.85 -161.95 REMARK 500 SER A 538 -126.26 41.16 REMARK 500 ASP A 557 70.94 -161.31 REMARK 500 ASN A 688 98.47 -167.71 REMARK 500 PHE A 695 58.71 39.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 195 0.08 SIDE CHAIN REMARK 500 ARG A 404 0.12 SIDE CHAIN REMARK 500 TYR A 514 0.07 SIDE CHAIN REMARK 500 ARG A 663 0.09 SIDE CHAIN 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 A1751 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BIX A 1 O61 REMARK 620 2 ASP A 377 OD2 99.8 REMARK 620 3 GLU A 415 OE2 138.9 100.2 REMARK 620 4 HIS A 543 NE2 101.8 99.9 109.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1752 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 BIX A 1 O6 REMARK 620 2 HIS A 367 NE2 102.4 REMARK 620 3 ASP A 377 OD1 109.5 98.3 REMARK 620 4 ASP A 443 OD1 152.4 88.5 93.6 REMARK 620 5 ASP A 443 OD2 97.7 91.1 148.4 56.3 REMARK 620 6 HOH A1262 O 92.8 164.7 78.2 76.9 84.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1755 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 259 O REMARK 620 2 THR A 259 OG1 72.0 REMARK 620 3 TYR A 262 O 73.9 90.6 REMARK 620 4 GLU A 423 OE1 152.0 90.1 85.2 REMARK 620 5 GLU A 423 OE2 150.0 100.4 135.9 52.7 REMARK 620 6 GLU A 426 OE2 103.6 169.7 79.2 90.2 87.9 REMARK 620 7 HOH A 928 O 73.9 90.1 145.9 129.0 77.2 97.6 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FF3 RELATED DB: PDB REMARK 900 RELATED ID: 3FEC RELATED DB: PDB REMARK 900 RELATED ID: 3FEE RELATED DB: PDB DBREF 3FED A 36 740 UNP Q9Y3Q0 NALD2_HUMAN 36 740 SEQADV 3FED ARG A 34 UNP Q9Y3Q0 EXPRESSION TAG SEQADV 3FED SER A 35 UNP Q9Y3Q0 EXPRESSION TAG SEQRES 1 A 707 ARG SER GLU THR THR THR SER VAL ARG TYR HIS GLN SER SEQRES 2 A 707 ILE ARG TRP LYS LEU VAL SER GLU MET LYS ALA GLU ASN SEQRES 3 A 707 ILE LYS SER PHE LEU ARG SER PHE THR LYS LEU PRO HIS SEQRES 4 A 707 LEU ALA GLY THR GLU GLN ASN PHE LEU LEU ALA LYS LYS SEQRES 5 A 707 ILE GLN THR GLN TRP LYS LYS PHE GLY LEU ASP SER ALA SEQRES 6 A 707 LYS LEU VAL HIS TYR ASP VAL LEU LEU SER TYR PRO ASN SEQRES 7 A 707 GLU THR ASN ALA ASN TYR ILE SER ILE VAL ASP GLU HIS SEQRES 8 A 707 GLU THR GLU ILE PHE LYS THR SER TYR LEU GLU PRO PRO SEQRES 9 A 707 PRO ASP GLY TYR GLU ASN VAL THR ASN ILE VAL PRO PRO SEQRES 10 A 707 TYR ASN ALA PHE SER ALA GLN GLY MET PRO GLU GLY ASP SEQRES 11 A 707 LEU VAL TYR VAL ASN TYR ALA ARG THR GLU ASP PHE PHE SEQRES 12 A 707 LYS LEU GLU ARG GLU MET GLY ILE ASN CYS THR GLY LYS SEQRES 13 A 707 ILE VAL ILE ALA ARG TYR GLY LYS ILE PHE ARG GLY ASN SEQRES 14 A 707 LYS VAL LYS ASN ALA MET LEU ALA GLY ALA ILE GLY ILE SEQRES 15 A 707 ILE LEU TYR SER ASP PRO ALA ASP TYR PHE ALA PRO GLU SEQRES 16 A 707 VAL GLN PRO TYR PRO LYS GLY TRP ASN LEU PRO GLY THR SEQRES 17 A 707 ALA ALA GLN ARG GLY ASN VAL LEU ASN LEU ASN GLY ALA SEQRES 18 A 707 GLY ASP PRO LEU THR PRO GLY TYR PRO ALA LYS GLU TYR SEQRES 19 A 707 THR PHE ARG LEU ASP VAL GLU GLU GLY VAL GLY ILE PRO SEQRES 20 A 707 ARG ILE PRO VAL HIS PRO ILE GLY TYR ASN ASP ALA GLU SEQRES 21 A 707 ILE LEU LEU ARG TYR LEU GLY GLY ILE ALA PRO PRO ASP SEQRES 22 A 707 LYS SER TRP LYS GLY ALA LEU ASN VAL SER TYR SER ILE SEQRES 23 A 707 GLY PRO GLY PHE THR GLY SER ASP SER PHE ARG LYS VAL SEQRES 24 A 707 ARG MET HIS VAL TYR ASN ILE ASN LYS ILE THR ARG ILE SEQRES 25 A 707 TYR ASN VAL VAL GLY THR ILE ARG GLY SER VAL GLU PRO SEQRES 26 A 707 ASP ARG TYR VAL ILE LEU GLY GLY HIS ARG ASP SER TRP SEQRES 27 A 707 VAL PHE GLY ALA ILE ASP PRO THR SER GLY VAL ALA VAL SEQRES 28 A 707 LEU GLN GLU ILE ALA ARG SER PHE GLY LYS LEU MET SER SEQRES 29 A 707 LYS GLY TRP ARG PRO ARG ARG THR ILE ILE PHE ALA SER SEQRES 30 A 707 TRP ASP ALA GLU GLU PHE GLY LEU LEU GLY SER THR GLU SEQRES 31 A 707 TRP ALA GLU GLU ASN VAL LYS ILE LEU GLN GLU ARG SER SEQRES 32 A 707 ILE ALA TYR ILE ASN SER ASP SER SER ILE GLU GLY ASN SEQRES 33 A 707 TYR THR LEU ARG VAL ASP CYS THR PRO LEU LEU TYR GLN SEQRES 34 A 707 LEU VAL TYR LYS LEU THR LYS GLU ILE PRO SER PRO ASP SEQRES 35 A 707 ASP GLY PHE GLU SER LYS SER LEU TYR GLU SER TRP LEU SEQRES 36 A 707 GLU LYS ASP PRO SER PRO GLU ASN LYS ASN LEU PRO ARG SEQRES 37 A 707 ILE ASN LYS LEU GLY SER GLY SER ASP PHE GLU ALA TYR SEQRES 38 A 707 PHE GLN ARG LEU GLY ILE ALA SER GLY ARG ALA ARG TYR SEQRES 39 A 707 THR LYS ASN LYS LYS THR ASP LYS TYR SER SER TYR PRO SEQRES 40 A 707 VAL TYR HIS THR ILE TYR GLU THR PHE GLU LEU VAL GLU SEQRES 41 A 707 LYS PHE TYR ASP PRO THR PHE LYS LYS GLN LEU SER VAL SEQRES 42 A 707 ALA GLN LEU ARG GLY ALA LEU VAL TYR GLU LEU VAL ASP SEQRES 43 A 707 SER LYS ILE ILE PRO PHE ASN ILE GLN ASP TYR ALA GLU SEQRES 44 A 707 ALA LEU LYS ASN TYR ALA ALA SER ILE TYR ASN LEU SER SEQRES 45 A 707 LYS LYS HIS ASP GLN GLN LEU THR ASP HIS GLY VAL SER SEQRES 46 A 707 PHE ASP SER LEU PHE SER ALA VAL LYS ASN PHE SER GLU SEQRES 47 A 707 ALA ALA SER ASP PHE HIS LYS ARG LEU ILE GLN VAL ASP SEQRES 48 A 707 LEU ASN ASN PRO ILE ALA VAL ARG MET MET ASN ASP GLN SEQRES 49 A 707 LEU MET LEU LEU GLU ARG ALA PHE ILE ASP PRO LEU GLY SEQRES 50 A 707 LEU PRO GLY LYS LEU PHE TYR ARG HIS ILE ILE PHE ALA SEQRES 51 A 707 PRO SER SER HIS ASN LYS TYR ALA GLY GLU SER PHE PRO SEQRES 52 A 707 GLY ILE TYR ASP ALA ILE PHE ASP ILE GLU ASN LYS ALA SEQRES 53 A 707 ASN SER ARG LEU ALA TRP LYS GLU VAL LYS LYS HIS ILE SEQRES 54 A 707 SER ILE ALA ALA PHE THR ILE GLN ALA ALA ALA GLY THR SEQRES 55 A 707 LEU LYS GLU VAL LEU MODRES 3FED ASN A 111 ASN GLYCOSYLATION SITE MODRES 3FED ASN A 185 ASN GLYCOSYLATION SITE MODRES 3FED ASN A 449 ASN GLYCOSYLATION SITE MODRES 3FED ASN A 628 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET NAG A1756 14 HET NAG A1757 14 HET NAG A1758 14 HET ZN A1751 1 HET ZN A1752 1 HET CL A1754 1 HET CA A1755 1 HET BIX A 1 20 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM CA CALCIUM ION HETNAM BIX (2S)-2-{[(S)-[(3S)-3-AMINO-3-CARBOXYPROPYL](HYDROXY) HETNAM 2 BIX PHOSPHORYL]METHYL}PENTANEDIOIC ACID HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 6 ZN 2(ZN 2+) FORMUL 8 CL CL 1- FORMUL 9 CA CA 2+ FORMUL 10 BIX C10 H18 N O8 P FORMUL 11 HOH *861(H2 O) HELIX 1 1 SER A 46 MET A 55 1 10 HELIX 2 2 LYS A 56 THR A 68 1 13 HELIX 3 3 THR A 76 GLY A 94 1 19 HELIX 4 4 ARG A 171 GLU A 181 1 11 HELIX 5 5 PHE A 199 ALA A 210 1 12 HELIX 6 6 ASP A 220 PHE A 225 1 6 HELIX 7 7 ASP A 272 GLY A 276 5 5 HELIX 8 8 GLY A 288 TYR A 298 1 11 HELIX 9 9 ASP A 306 LYS A 310 5 5 HELIX 10 10 PRO A 378 LYS A 398 1 21 HELIX 11 11 ALA A 413 GLY A 417 5 5 HELIX 12 12 LEU A 418 ARG A 435 1 18 HELIX 13 13 LEU A 460 LYS A 469 1 10 HELIX 14 14 SER A 482 ASP A 491 1 10 HELIX 15 15 PHE A 511 ARG A 517 1 7 HELIX 16 16 THR A 548 TYR A 556 1 9 HELIX 17 17 PHE A 560 SER A 580 1 21 HELIX 18 18 ASN A 586 LYS A 606 1 21 HELIX 19 19 HIS A 608 GLY A 616 1 9 HELIX 20 20 PHE A 619 ILE A 641 1 23 HELIX 21 21 ASN A 647 PHE A 665 1 19 HELIX 22 22 PHE A 695 PHE A 703 1 9 HELIX 23 23 ASP A 704 LYS A 708 5 5 HELIX 24 24 ASN A 710 LYS A 737 1 28 SHEET 1 A 8 SER A 97 TYR A 109 0 SHEET 2 A 8 ILE A 339 ILE A 352 -1 O ASN A 347 N VAL A 101 SHEET 3 A 8 ARG A 404 TRP A 411 -1 O PHE A 408 N GLY A 350 SHEET 4 A 8 GLU A 357 HIS A 367 1 N LEU A 364 O ILE A 407 SHEET 5 A 8 SER A 436 ASN A 441 1 O ILE A 437 N TYR A 361 SHEET 6 A 8 SER A 522 THR A 528 1 O GLY A 523 N ASN A 441 SHEET 7 A 8 THR A 451 CYS A 456 -1 N THR A 451 O THR A 528 SHEET 8 A 8 ILE A 502 ASN A 503 1 O ASN A 503 N VAL A 454 SHEET 1 B 4 GLU A 127 LYS A 130 0 SHEET 2 B 4 TYR A 117 VAL A 121 -1 N ILE A 120 O ILE A 128 SHEET 3 B 4 LYS A 331 HIS A 335 -1 O ARG A 333 N SER A 119 SHEET 4 B 4 GLU A 161 GLY A 162 -1 N GLY A 162 O VAL A 332 SHEET 1 C 4 LEU A 164 TYR A 166 0 SHEET 2 C 4 ILE A 190 ARG A 194 1 O ILE A 192 N VAL A 165 SHEET 3 C 4 GLY A 214 TYR A 218 1 O ILE A 216 N VAL A 191 SHEET 4 C 4 VAL A 284 ILE A 287 1 O ILE A 287 N LEU A 217 SHEET 1 D 2 PRO A 492 SER A 493 0 SHEET 2 D 2 ASN A 496 PRO A 500 -1 O LEU A 499 N SER A 493 SHEET 1 E 2 PHE A 682 SER A 685 0 SHEET 2 E 2 ASN A 688 SER A 694 -1 O ALA A 691 N SER A 685 LINK ND2 ASN A 111 C1 NAG A1756 1555 1555 1.45 LINK ND2 ASN A 185 C1 NAG A1757 1555 1555 1.39 LINK ND2 ASN A 449 C1 NAG A1758 1555 1555 1.43 LINK ND2 ASN A 628 C1 NAG B 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.43 LINK O61 BIX A 1 ZN ZN A1751 1555 1555 1.94 LINK O6 BIX A 1 ZN ZN A1752 1555 1555 2.07 LINK O THR A 259 CA CA A1755 1555 1555 2.44 LINK OG1 THR A 259 CA CA A1755 1555 1555 2.46 LINK O TYR A 262 CA CA A1755 1555 1555 2.34 LINK NE2 HIS A 367 ZN ZN A1752 1555 1555 2.12 LINK OD2 ASP A 377 ZN ZN A1751 1555 1555 1.98 LINK OD1 ASP A 377 ZN ZN A1752 1555 1555 2.03 LINK OE2 GLU A 415 ZN ZN A1751 1555 1555 2.00 LINK OE1 GLU A 423 CA CA A1755 1555 1555 2.46 LINK OE2 GLU A 423 CA CA A1755 1555 1555 2.49 LINK OE2 GLU A 426 CA CA A1755 1555 1555 2.30 LINK OD1 ASP A 443 ZN ZN A1752 1555 1555 2.32 LINK OD2 ASP A 443 ZN ZN A1752 1555 1555 2.32 LINK NE2 HIS A 543 ZN ZN A1751 1555 1555 2.03 LINK O HOH A 928 CA CA A1755 1555 1555 2.36 LINK O HOH A1262 ZN ZN A1752 1555 1555 2.24 CISPEP 1 TYR A 232 PRO A 233 0 9.06 CISPEP 2 GLY A 320 PRO A 321 0 5.43 CISPEP 3 ASP A 377 PRO A 378 0 1.68 CRYST1 122.731 104.086 77.634 90.00 108.19 90.00 C 1 2 1 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 0.008148 0.000000 0.002678 0.00000 SCALE2 0.000000 0.009607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013559 0.00000