PDB Short entry for 2O4H HEADER HYDROLASE 04-DEC-06 2O4H TITLE HUMAN BRAIN ASPARTOACYLASE COMPLEX WITH INTERMEDIATE ANALOG (N- TITLE 2 PHOSPHONOMETHYL-L-ASPARTATE) 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 ORGAN: BRAIN; 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; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPICZA KEYWDS CANAVAN DISEASE, N-ACETYL-L-ASPARTATE, ZINC-DEPENDENT HYDROLASE, KEYWDS 2 ASPARTOACYLASE FAMILY, HYDROLASE, AMINOACYLASE-2, ACY2, ASPA, N- KEYWDS 3 PHOSPHONOMETHYL-L-ASPARTATE EXPDTA X-RAY DIFFRACTION AUTHOR J.LE COQ,A.PAVLOVSKY,R.SANISHVILI,R.E.VIOLA REVDAT 4 30-AUG-23 2O4H 1 REMARK REVDAT 3 13-JUL-11 2O4H 1 VERSN REVDAT 2 25-MAR-08 2O4H 1 JRNL VERSN REVDAT 1 06-NOV-07 2O4H 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) : 46.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 27490 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1449 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) : 1229 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4842 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 69 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 72.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -1.16000 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): 0.451 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.321 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.250 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.812 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4988 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6762 ; 1.639 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 600 ; 7.269 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 234 ;38.018 ;24.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 870 ;19.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;10.473 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 740 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3788 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2181 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3365 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 175 ; 0.145 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.042 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 24 ; 0.185 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.067 ; 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): 3105 ; 0.748 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4920 ; 1.346 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2106 ; 1.639 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1842 ; 2.779 ; 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 10 A 310 REMARK 3 RESIDUE RANGE : B 10 B 310 REMARK 3 ORIGIN FOR THE GROUP (A): -43.7620 15.6990 -30.2540 REMARK 3 T TENSOR REMARK 3 T11: 0.0602 T22: 0.0526 REMARK 3 T33: -0.2243 T12: -0.0143 REMARK 3 T13: 0.0014 T23: -0.0349 REMARK 3 L TENSOR REMARK 3 L11: 0.6334 L22: 0.6853 REMARK 3 L33: 1.3114 L12: 0.1036 REMARK 3 L13: -0.1182 L23: 0.4196 REMARK 3 S TENSOR REMARK 3 S11: -0.0743 S12: 0.0260 S13: -0.0588 REMARK 3 S21: -0.0088 S22: -0.0945 S23: 0.1109 REMARK 3 S31: -0.0735 S32: 0.0529 S33: 0.1688 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 2O4H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040675. 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) : 1.28300 REMARK 200 MONOCHROMATOR : NULL 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 : 27490 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 (%) : 95.3 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000 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 (%) : 62.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: PDB ENTRY 2I3C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8-10 MG/ML PROTEIN, 50 MM SODIUM REMARK 280 CITRATE PH 6.0, 300 MM K2HPO4, 15-19% PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.0K 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 71.54050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 71.54050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.30200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 71.54050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 71.54050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.30200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 71.54050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.54050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.30200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 71.54050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.54050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.30200 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 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 503 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 515 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 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 GLU A 9 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 GLU B 9 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: 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 0.231 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 GLU A 158 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 PRO A 160 C - N - CA ANGL. DEV. = 34.7 DEGREES REMARK 500 PRO A 160 C - N - CD ANGL. DEV. = -33.5 DEGREES REMARK 500 PRO B 160 C - N - CA ANGL. DEV. = 14.5 DEGREES REMARK 500 LEU B 301 CA - CB - CG ANGL. DEV. = 16.1 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 HIS A 159 153.81 3.09 REMARK 500 PRO A 160 -73.34 48.85 REMARK 500 GLU A 211 24.11 -76.61 REMARK 500 TRP A 252 -31.49 72.10 REMARK 500 PRO A 257 -38.46 -36.03 REMARK 500 ASN B 54 69.64 -119.58 REMARK 500 CYS B 61 62.08 29.86 REMARK 500 ILE B 65 -66.14 -91.66 REMARK 500 ILE B 157 30.00 -96.35 REMARK 500 PRO B 160 -87.65 28.37 REMARK 500 TRP B 252 -18.95 74.86 REMARK 500 MET B 261 -41.58 -135.89 REMARK 500 LYS B 292 70.76 52.94 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 ILE A 157 GLU A 158 139.95 REMARK 500 HIS A 159 PRO A 160 41.24 REMARK 500 HIS B 159 PRO B 160 71.42 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 21 ND1 REMARK 620 2 GLU A 24 OE1 114.3 REMARK 620 3 HIS A 116 ND1 102.4 98.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 21 ND1 REMARK 620 2 GLU B 24 OE1 118.1 REMARK 620 3 HIS B 116 ND1 100.3 101.3 REMARK 620 4 AS9 B 501 OAG 80.4 124.9 127.5 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AS9 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AS9 B 501 DBREF 2O4H A 1 313 UNP P45381 ACY2_HUMAN 1 313 DBREF 2O4H 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 401 1 HET AS9 A 501 13 HET ZN B 401 1 HET AS9 B 501 13 HETNAM ZN ZINC ION HETNAM AS9 N-[HYDROXY(METHYL)PHOSPHORYL]-L-ASPARTIC ACID HETSYN AS9 N-PHOSPHONOMETHYL-L-ASPARTIC ACID; (2S)-2- HETSYN 2 AS9 (HYDROPEROXY(METHOXY)PHOSPHORYLAMINO)SUCCINIC ACID FORMUL 3 ZN 2(ZN 2+) FORMUL 4 AS9 2(C5 H10 N O6 P) FORMUL 7 HOH *69(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 CYS A 61 1 8 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 153 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 MET A 261 SHEET 1 C 9 VAL B 48 ILE B 52 0 SHEET 2 C 9 VAL B 14 GLY B 18 1 N ILE B 16 O LYS B 49 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 ASP B 114 SHEET 5 C 9 GLY B 123 LEU B 128 -1 N THR B 125 O GLU B 178 SHEET 6 C 9 TYR B 153 LEU B 156 1 O TYR B 153 N LEU B 126 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 401 1555 1555 2.23 LINK OE1 GLU A 24 ZN ZN A 401 1555 1555 2.15 LINK ND1 HIS A 116 ZN ZN A 401 1555 1555 2.29 LINK ND1 HIS B 21 ZN ZN B 401 1555 1555 2.03 LINK OE1 GLU B 24 ZN ZN B 401 1555 1555 1.97 LINK ND1 HIS B 116 ZN ZN B 401 1555 1555 2.39 LINK ZN ZN B 401 OAG AS9 B 501 1555 1555 2.16 CISPEP 1 GLY A 101 PRO A 102 0 -5.74 CISPEP 2 ALA A 148 PRO A 149 0 7.88 CISPEP 3 GLU A 158 HIS A 159 0 11.72 CISPEP 4 GLY A 180 PRO A 181 0 7.83 CISPEP 5 GLY B 101 PRO B 102 0 -9.38 CISPEP 6 ALA B 148 PRO B 149 0 9.58 CISPEP 7 GLY B 180 PRO B 181 0 5.23 CISPEP 8 ASP B 266 GLY B 267 0 -6.38 SITE 1 AC1 4 HIS A 21 GLU A 24 HIS A 116 AS9 A 501 SITE 1 AC2 4 HIS B 21 GLU B 24 HIS B 116 AS9 B 501 SITE 1 AC3 14 HIS A 21 GLU A 24 ARG A 63 ASN A 70 SITE 2 AC3 14 ARG A 71 HIS A 116 ASN A 117 ILE A 127 SITE 3 AC3 14 TYR A 164 ARG A 168 GLU A 178 GLU A 285 SITE 4 AC3 14 TYR A 288 ZN A 401 SITE 1 AC4 13 HIS B 21 GLU B 24 ARG B 63 ASN B 70 SITE 2 AC4 13 ARG B 71 HIS B 116 ASN B 117 TYR B 164 SITE 3 AC4 13 ARG B 168 GLU B 178 GLU B 285 TYR B 288 SITE 4 AC4 13 ZN B 401 CRYST1 143.081 143.081 104.604 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 0.006989 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009560 0.00000