HEADER HYDROLASE 05-DEC-06 2O53 TITLE CRYSTAL STRUCTURE OF APO-ASPARTOACYLASE FROM HUMAN BRAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTOACYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: AMINOACYLASE-2, ACY-2; COMPND 5 EC: 3.5.1.15; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: HUMAN; SOURCE 6 GENE: ASPA, ACY2, ASP; SOURCE 7 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: KM71H; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID/HOMOLOGOUS RECOMBINATION; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPICZ A KEYWDS CANAVAN DISEASE, N-ACETYL-L-ASPARTATE, ZINC-DEPENDENT HYDROLASE, KEYWDS 2 ASPARTOACYLASE FAMILY, AMINOACYLASE-2, ACY2, ASPA, N- KEYWDS 3 PHOSPHONOMETHYL-L-ASPARTATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.LE COQ,A.PAVLOVSKY,R.SANISHVILI,R.E.VIOLA REVDAT 5 30-AUG-23 2O53 1 REMARK LINK REVDAT 4 13-JUL-11 2O53 1 VERSN REVDAT 3 24-FEB-09 2O53 1 VERSN REVDAT 2 01-APR-08 2O53 1 JRNL REVDAT 1 06-NOV-07 2O53 0 JRNL AUTH J.LE COQ,A.PAVLOVSKY,R.MALIK,R.SANISHVILI,C.XU,R.E.VIOLA JRNL TITL EXAMINATION OF THE MECHANISM OF HUMAN BRAIN ASPARTOACYLASE JRNL TITL 2 THROUGH THE BINDING OF AN INTERMEDIATE ANALOGUE. JRNL REF BIOCHEMISTRY V. 47 3484 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18293939 JRNL DOI 10.1021/BI702400X REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 81.3 REMARK 3 NUMBER OF REFLECTIONS : 23564 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1260 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 847 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 39.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.4540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 65.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.08000 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): 0.713 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.361 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.273 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.286 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4998 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6776 ; 1.469 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 602 ; 6.987 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 236 ;39.067 ;24.492 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 874 ;19.593 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.162 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 738 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3788 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2215 ; 0.225 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3367 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 166 ; 0.144 ; 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): 25 ; 0.209 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.538 ; 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): 3110 ; 0.627 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4914 ; 1.111 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2120 ; 1.286 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1862 ; 2.041 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 9 A 310 REMARK 3 RESIDUE RANGE : B 9 B 310 REMARK 3 ORIGIN FOR THE GROUP (A): -44.0260 16.0120 -30.0200 REMARK 3 T TENSOR REMARK 3 T11: 0.2721 T22: 0.2556 REMARK 3 T33: -0.1826 T12: 0.0178 REMARK 3 T13: -0.0150 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.1495 L22: 1.3037 REMARK 3 L33: 2.2772 L12: 0.2106 REMARK 3 L13: -0.1785 L23: 0.7185 REMARK 3 S TENSOR REMARK 3 S11: -0.1063 S12: 0.0396 S13: -0.1005 REMARK 3 S21: -0.0390 S22: -0.1126 S23: 0.1315 REMARK 3 S31: -0.0665 S32: 0.0313 S33: 0.2189 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 2O53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040697. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-06 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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF REMARK 200 FOCUSING BIMORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26648 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 87.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 47.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30600 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 2O4H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION 8-10 MG/ML, 0.05 REMARK 280 M SODIUM CITRATE PH 6.0, 0.3 M K2HPO4, 19% PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 71.89700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 71.89700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.03800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 71.89700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 71.89700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.03800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 71.89700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.89700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.03800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 71.89700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.89700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.03800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE TWO FOLD AXIS: -X, -Y, Z. 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 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 MET A 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 CYS A 4 REMARK 465 HIS A 5 REMARK 465 ILE A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 CYS A 311 REMARK 465 LEU A 312 REMARK 465 HIS A 313 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 SER B 3 REMARK 465 CYS B 4 REMARK 465 HIS B 5 REMARK 465 ILE B 6 REMARK 465 ALA B 7 REMARK 465 GLU B 8 REMARK 465 CYS B 311 REMARK 465 LEU B 312 REMARK 465 HIS B 313 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 324 O HOH A 324 8554 1.60 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 CYS B 310 C CYS B 310 O 0.516 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 PRO B 160 C - N - CA ANGL. DEV. = 19.8 DEGREES REMARK 500 PRO B 160 C - N - CD ANGL. DEV. = -15.1 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 THR A 44 106.81 -55.08 REMARK 500 GLU A 84 -2.43 -58.84 REMARK 500 HIS A 159 -162.83 -113.76 REMARK 500 SER A 161 -14.52 -145.56 REMARK 500 ILE A 226 -42.23 -135.36 REMARK 500 GLU A 235 6.13 -66.69 REMARK 500 TRP A 252 -25.75 78.70 REMARK 500 PRO A 257 -53.70 -27.88 REMARK 500 MET A 261 -51.23 -129.26 REMARK 500 ASN A 284 45.01 72.13 REMARK 500 LYS A 291 15.35 -66.03 REMARK 500 LYS A 292 92.74 44.76 REMARK 500 GLU A 293 136.28 -172.92 REMARK 500 PRO B 87 152.14 -49.76 REMARK 500 HIS B 159 -104.41 -115.65 REMARK 500 PRO B 160 -94.88 -12.01 REMARK 500 SER B 161 -80.71 -56.97 REMARK 500 LEU B 162 48.88 -51.37 REMARK 500 ALA B 165 17.79 89.85 REMARK 500 GLU B 227 136.99 -172.19 REMARK 500 TRP B 252 -20.53 77.20 REMARK 500 PRO B 257 -47.39 -23.43 REMARK 500 MET B 261 -54.15 -131.54 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 GLU A 158 HIS A 159 50.40 REMARK 500 HIS A 159 PRO A 160 -70.76 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 A 314 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 21 ND1 REMARK 620 2 GLU A 24 OE1 113.8 REMARK 620 3 HIS A 116 ND1 104.6 91.9 REMARK 620 4 PO4 A 315 O4 129.8 94.7 115.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 314 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 21 ND1 REMARK 620 2 GLU B 24 OE1 108.8 REMARK 620 3 HIS B 116 ND1 99.6 92.4 REMARK 620 4 PO4 B 315 O1 140.9 103.8 100.2 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 ZN A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 316 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2O4H RELATED DB: PDB REMARK 900 COMPLEX CRYSTAL STRUCTURE OF HUMAN ASPARTOACYLASE WITH INTERMEDIATE REMARK 900 ANALOG (N-PHOSPHONOMETHYL-L-ASPARTATE) DBREF 2O53 A 1 313 UNP P45381 ACY2_HUMAN 1 313 DBREF 2O53 B 1 313 UNP P45381 ACY2_HUMAN 1 313 SEQRES 1 A 313 MET THR SER CYS HIS ILE ALA GLU GLU HIS ILE GLN LYS SEQRES 2 A 313 VAL ALA ILE PHE GLY GLY THR HIS GLY ASN GLU LEU THR SEQRES 3 A 313 GLY VAL PHE LEU VAL LYS HIS TRP LEU GLU ASN GLY ALA SEQRES 4 A 313 GLU ILE GLN ARG THR GLY LEU GLU VAL LYS PRO PHE ILE SEQRES 5 A 313 THR ASN PRO ARG ALA VAL LYS LYS CYS THR ARG TYR ILE SEQRES 6 A 313 ASP CYS ASP LEU ASN ARG ILE PHE ASP LEU GLU ASN LEU SEQRES 7 A 313 GLY LYS LYS MET SER GLU ASP LEU PRO TYR GLU VAL ARG SEQRES 8 A 313 ARG ALA GLN GLU ILE ASN HIS LEU PHE GLY PRO LYS ASP SEQRES 9 A 313 SER GLU ASP SER TYR ASP ILE ILE PHE ASP LEU HIS ASN SEQRES 10 A 313 THR THR SER ASN MET GLY CYS THR LEU ILE LEU GLU ASP SEQRES 11 A 313 SER ARG ASN ASN PHE LEU ILE GLN MET PHE HIS TYR ILE SEQRES 12 A 313 LYS THR SER LEU ALA PRO LEU PRO CYS TYR VAL TYR LEU SEQRES 13 A 313 ILE GLU HIS PRO SER LEU LYS TYR ALA THR THR ARG SER SEQRES 14 A 313 ILE ALA LYS TYR PRO VAL GLY ILE GLU VAL GLY PRO GLN SEQRES 15 A 313 PRO GLN GLY VAL LEU ARG ALA ASP ILE LEU ASP GLN MET SEQRES 16 A 313 ARG LYS MET ILE LYS HIS ALA LEU ASP PHE ILE HIS HIS SEQRES 17 A 313 PHE ASN GLU GLY LYS GLU PHE PRO PRO CYS ALA ILE GLU SEQRES 18 A 313 VAL TYR LYS ILE ILE GLU LYS VAL ASP TYR PRO ARG ASP SEQRES 19 A 313 GLU ASN GLY GLU ILE ALA ALA ILE ILE HIS PRO ASN LEU SEQRES 20 A 313 GLN ASP GLN ASP TRP LYS PRO LEU HIS PRO GLY ASP PRO SEQRES 21 A 313 MET PHE LEU THR LEU ASP GLY LYS THR ILE PRO LEU GLY SEQRES 22 A 313 GLY ASP CYS THR VAL TYR PRO VAL PHE VAL ASN GLU ALA SEQRES 23 A 313 ALA TYR TYR GLU LYS LYS GLU ALA PHE ALA LYS THR THR SEQRES 24 A 313 LYS LEU THR LEU ASN ALA LYS SER ILE ARG CYS CYS LEU SEQRES 25 A 313 HIS SEQRES 1 B 313 MET THR SER CYS HIS ILE ALA GLU GLU HIS ILE GLN LYS SEQRES 2 B 313 VAL ALA ILE PHE GLY GLY THR HIS GLY ASN GLU LEU THR SEQRES 3 B 313 GLY VAL PHE LEU VAL LYS HIS TRP LEU GLU ASN GLY ALA SEQRES 4 B 313 GLU ILE GLN ARG THR GLY LEU GLU VAL LYS PRO PHE ILE SEQRES 5 B 313 THR ASN PRO ARG ALA VAL LYS LYS CYS THR ARG TYR ILE SEQRES 6 B 313 ASP CYS ASP LEU ASN ARG ILE PHE ASP LEU GLU ASN LEU SEQRES 7 B 313 GLY LYS LYS MET SER GLU ASP LEU PRO TYR GLU VAL ARG SEQRES 8 B 313 ARG ALA GLN GLU ILE ASN HIS LEU PHE GLY PRO LYS ASP SEQRES 9 B 313 SER GLU ASP SER TYR ASP ILE ILE PHE ASP LEU HIS ASN SEQRES 10 B 313 THR THR SER ASN MET GLY CYS THR LEU ILE LEU GLU ASP SEQRES 11 B 313 SER ARG ASN ASN PHE LEU ILE GLN MET PHE HIS TYR ILE SEQRES 12 B 313 LYS THR SER LEU ALA PRO LEU PRO CYS TYR VAL TYR LEU SEQRES 13 B 313 ILE GLU HIS PRO SER LEU LYS TYR ALA THR THR ARG SER SEQRES 14 B 313 ILE ALA LYS TYR PRO VAL GLY ILE GLU VAL GLY PRO GLN SEQRES 15 B 313 PRO GLN GLY VAL LEU ARG ALA ASP ILE LEU ASP GLN MET SEQRES 16 B 313 ARG LYS MET ILE LYS HIS ALA LEU ASP PHE ILE HIS HIS SEQRES 17 B 313 PHE ASN GLU GLY LYS GLU PHE PRO PRO CYS ALA ILE GLU SEQRES 18 B 313 VAL TYR LYS ILE ILE GLU LYS VAL ASP TYR PRO ARG ASP SEQRES 19 B 313 GLU ASN GLY GLU ILE ALA ALA ILE ILE HIS PRO ASN LEU SEQRES 20 B 313 GLN ASP GLN ASP TRP LYS PRO LEU HIS PRO GLY ASP PRO SEQRES 21 B 313 MET PHE LEU THR LEU ASP GLY LYS THR ILE PRO LEU GLY SEQRES 22 B 313 GLY ASP CYS THR VAL TYR PRO VAL PHE VAL ASN GLU ALA SEQRES 23 B 313 ALA TYR TYR GLU LYS LYS GLU ALA PHE ALA LYS THR THR SEQRES 24 B 313 LYS LEU THR LEU ASN ALA LYS SER ILE ARG CYS CYS LEU SEQRES 25 B 313 HIS HET ZN A 314 1 HET PO4 A 315 5 HET PO4 A 316 5 HET ZN B 314 1 HET PO4 B 315 5 HET PO4 B 316 5 HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION FORMUL 3 ZN 2(ZN 2+) FORMUL 4 PO4 4(O4 P 3-) FORMUL 9 HOH *30(H2 O) HELIX 1 1 GLU A 24 LEU A 35 1 12 HELIX 2 2 GLY A 38 GLN A 42 5 5 HELIX 3 3 ASN A 54 LYS A 60 1 7 HELIX 4 4 ASP A 68 ILE A 72 5 5 HELIX 5 5 ASP A 74 GLY A 79 1 6 HELIX 6 6 PRO A 87 GLY A 101 1 15 HELIX 7 7 ASN A 133 ALA A 148 1 16 HELIX 8 8 THR A 166 ALA A 171 5 6 HELIX 9 9 ARG A 188 GLU A 211 1 24 HELIX 10 10 GLU A 285 TYR A 289 5 5 HELIX 11 11 GLU B 24 ASN B 37 1 14 HELIX 12 12 GLY B 38 GLN B 42 5 5 HELIX 13 13 ASN B 54 LYS B 60 1 7 HELIX 14 14 ASP B 68 ILE B 72 5 5 HELIX 15 15 ASP B 74 GLY B 79 1 6 HELIX 16 16 PRO B 87 GLY B 101 1 15 HELIX 17 17 ASN B 133 ALA B 148 1 16 HELIX 18 18 THR B 166 ALA B 171 5 6 HELIX 19 19 ARG B 188 GLU B 211 1 24 HELIX 20 20 GLU B 285 TYR B 289 5 5 SHEET 1 A 9 GLU A 47 ILE A 52 0 SHEET 2 A 9 LYS A 13 GLY A 18 1 N ILE A 16 O LYS A 49 SHEET 3 A 9 ILE A 111 ASN A 117 1 O PHE A 113 N PHE A 17 SHEET 4 A 9 TYR A 173 GLY A 180 1 O ILE A 177 N HIS A 116 SHEET 5 A 9 GLY A 123 LEU A 128 -1 N THR A 125 O GLU A 178 SHEET 6 A 9 CYS A 152 LEU A 156 1 O TYR A 155 N LEU A 126 SHEET 7 A 9 CYS A 218 VAL A 229 1 O TYR A 223 N LEU A 156 SHEET 8 A 9 PHE A 295 ALA A 305 -1 O LYS A 297 N GLU A 227 SHEET 9 A 9 TYR A 279 VAL A 281 -1 N VAL A 281 O ALA A 296 SHEET 1 B 3 ILE A 242 ILE A 243 0 SHEET 2 B 3 PRO A 260 LEU A 263 -1 O LEU A 263 N ILE A 242 SHEET 3 B 3 THR A 269 PRO A 271 -1 O ILE A 270 N PHE A 262 SHEET 1 C 9 GLU B 47 ILE B 52 0 SHEET 2 C 9 LYS B 13 GLY B 18 1 N GLY B 18 O PHE B 51 SHEET 3 C 9 ILE B 111 ASN B 117 1 O PHE B 113 N PHE B 17 SHEET 4 C 9 TYR B 173 GLY B 180 1 O ILE B 177 N HIS B 116 SHEET 5 C 9 GLY B 123 LEU B 128 -1 N THR B 125 O GLU B 178 SHEET 6 C 9 CYS B 152 LEU B 156 1 O TYR B 155 N LEU B 128 SHEET 7 C 9 CYS B 218 VAL B 229 1 O TYR B 223 N LEU B 156 SHEET 8 C 9 PHE B 295 ALA B 305 -1 O LYS B 297 N GLU B 227 SHEET 9 C 9 TYR B 279 VAL B 281 -1 N VAL B 281 O ALA B 296 SHEET 1 D 3 ILE B 242 ILE B 243 0 SHEET 2 D 3 PRO B 260 LEU B 263 -1 O LEU B 263 N ILE B 242 SHEET 3 D 3 THR B 269 PRO B 271 -1 O ILE B 270 N PHE B 262 LINK ND1 HIS A 21 ZN ZN A 314 1555 1555 2.12 LINK OE1 GLU A 24 ZN ZN A 314 1555 1555 2.28 LINK ND1 HIS A 116 ZN ZN A 314 1555 1555 2.35 LINK ZN ZN A 314 O4 PO4 A 315 1555 1555 2.27 LINK ND1 HIS B 21 ZN ZN B 314 1555 1555 2.09 LINK OE1 GLU B 24 ZN ZN B 314 1555 1555 2.08 LINK ND1 HIS B 116 ZN ZN B 314 1555 1555 2.24 LINK ZN ZN B 314 O1 PO4 B 315 1555 1555 2.19 CISPEP 1 GLY A 101 PRO A 102 0 -4.41 CISPEP 2 ALA A 148 PRO A 149 0 7.52 CISPEP 3 GLY A 180 PRO A 181 0 5.08 CISPEP 4 GLY B 101 PRO B 102 0 -2.77 CISPEP 5 ALA B 148 PRO B 149 0 7.83 CISPEP 6 HIS B 159 PRO B 160 0 13.10 CISPEP 7 TYR B 164 ALA B 165 0 22.22 CISPEP 8 GLY B 180 PRO B 181 0 -3.97 CISPEP 9 ASP B 266 GLY B 267 0 -3.93 SITE 1 AC1 4 HIS A 21 GLU A 24 HIS A 116 PO4 A 315 SITE 1 AC2 10 HIS A 21 GLU A 24 ARG A 63 HIS A 116 SITE 2 AC2 10 ASN A 117 GLU A 178 TYR A 288 ZN A 314 SITE 3 AC2 10 PO4 A 316 HOH A 319 SITE 1 AC3 6 HIS A 21 ARG A 63 ASP A 68 ASN A 70 SITE 2 AC3 6 TYR A 288 PO4 A 315 SITE 1 AC4 4 HIS B 21 GLU B 24 HIS B 116 PO4 B 315 SITE 1 AC5 9 HIS B 21 GLU B 24 ARG B 63 HIS B 116 SITE 2 AC5 9 ASN B 117 GLU B 178 TYR B 288 ZN B 314 SITE 3 AC5 9 PO4 B 316 SITE 1 AC6 7 HIS B 21 ARG B 63 ASP B 68 ASN B 70 SITE 2 AC6 7 TYR B 164 TYR B 288 PO4 B 315 CRYST1 143.794 143.794 104.076 90.00 90.00 90.00 P 42 21 2 16 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 0.006954 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006954 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009608 0.00000