HEADER HYDROLASE 07-AUG-13 4M4V TITLE STRUCTURAL EVALUATION R171L MUTANT OF THE ASPERGILLUS FUMIGATUS KDNASE TITLE 2 (SIALIDASE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.2.1.18; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ASPERGILLUS FUMIGATUS; SOURCE 3 ORGANISM_TAXID: 330879; SOURCE 4 STRAIN: ATCC MYA-4609 / AF293 / CBS 101355 / FGSC A1100; SOURCE 5 GENE: AFUA_4G13800; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KDNASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.C.TELFORD,G.L.TAYLOR REVDAT 3 20-SEP-23 4M4V 1 HETSYN REVDAT 2 29-JUL-20 4M4V 1 REMARK SEQADV LINK SITE REVDAT 1 17-SEP-14 4M4V 0 JRNL AUTH J.Y.YEUNG,J.C.TELFORD,F.S SHIDMOOSSAVEE,A.J.BENNET, JRNL AUTH 2 G.L.TAYLOR,M.M.MOORE JRNL TITL ACTIVE SITE MUTANTS OF A FUNGAL KDNASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 70404 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3535 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) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4507 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 248 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 1188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.293 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6223 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8470 ; 1.201 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 805 ; 6.915 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 291 ;29.746 ;23.093 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 966 ;12.399 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 58 ;17.176 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 889 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4909 ; 0.006 ; 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): 3872 ; 0.496 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6201 ; 0.898 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2351 ; 1.418 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2252 ; 2.328 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4M4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081468. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70446 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.836 REMARK 200 RESOLUTION RANGE LOW (A) : 12.394 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.27800 REMARK 200 R SYM FOR SHELL (I) : 0.27800 REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2XCY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350, 0.2M SODIUM REMARK 280 NITRATE, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.98500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 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 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLN A 2 REMARK 465 SER A 3 REMARK 465 MET A 4 REMARK 465 ARG A 5 REMARK 465 PHE A 6 REMARK 465 MET A 7 REMARK 465 ILE A 8 REMARK 465 LEU A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 11 REMARK 465 LEU A 12 REMARK 465 VAL A 13 REMARK 465 GLN A 14 REMARK 465 PHE A 15 REMARK 465 LEU A 16 REMARK 465 PRO A 17 REMARK 465 ALA A 18 REMARK 465 TRP A 19 REMARK 465 ALA A 20 REMARK 465 ILE A 21 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 SER B 3 REMARK 465 MET B 4 REMARK 465 ARG B 5 REMARK 465 PHE B 6 REMARK 465 MET B 7 REMARK 465 ILE B 8 REMARK 465 LEU B 9 REMARK 465 ALA B 10 REMARK 465 LEU B 11 REMARK 465 LEU B 12 REMARK 465 VAL B 13 REMARK 465 GLN B 14 REMARK 465 PHE B 15 REMARK 465 LEU B 16 REMARK 465 PRO B 17 REMARK 465 ALA B 18 REMARK 465 TRP B 19 REMARK 465 ALA B 20 REMARK 465 ILE B 21 REMARK 465 ASN B 22 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 OD2 ASP B 84 O HOH B 1143 2.10 REMARK 500 O HOH A 1211 O HOH A 1212 2.12 REMARK 500 O HOH A 1212 O HOH A 1213 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 B 754 O HOH B 1072 2657 1.99 REMARK 500 O HOH A 1119 O HOH B 710 1554 2.11 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 SER A 117 N - CA - C ANGL. DEV. = 17.2 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 ILE A 60 63.63 64.16 REMARK 500 SER A 117 118.40 157.90 REMARK 500 SER A 117 -104.71 -110.03 REMARK 500 ALA A 201 -84.72 -110.56 REMARK 500 ASN A 235 44.48 -147.09 REMARK 500 ALA A 295 70.80 63.80 REMARK 500 ILE B 60 67.15 66.34 REMARK 500 ALA B 119 30.79 -98.73 REMARK 500 ALA B 201 -82.18 -110.22 REMARK 500 ASN B 235 44.50 -141.88 REMARK 500 ALA B 295 71.64 62.22 REMARK 500 ARG B 323 33.47 -96.65 REMARK 500 ASN B 405 2.91 90.64 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 GLY A 116 SER A 117 -126.59 REMARK 500 SER A 117 GLY A 118 148.12 REMARK 500 SER A 117 GLY A 118 -139.33 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 NA A 505 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 87 OD1 REMARK 620 2 ILE A 88 O 116.1 REMARK 620 3 ASN A 89 OD1 79.8 79.5 REMARK 620 4 SER A 117 O 79.4 163.8 99.9 REMARK 620 5 GLY A 120 O 107.1 91.3 170.4 88.1 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XCY RELATED DB: PDB REMARK 900 WILD TYPE APO AFS REMARK 900 RELATED ID: 2XZI RELATED DB: PDB REMARK 900 WILD TYPE AFS IN COMPLEX WITH KDN REMARK 900 RELATED ID: 2XZJ RELATED DB: PDB REMARK 900 WILD TYPE AFS IN COMPLEX WITH KDN2EN REMARK 900 RELATED ID: 2XZK RELATED DB: PDB REMARK 900 WILD TYPE AFS IN COMPLEX WITH KDF REMARK 900 RELATED ID: 4M4N RELATED DB: PDB REMARK 900 Y358H AFS MUTANT REMARK 900 RELATED ID: 4M4U RELATED DB: PDB REMARK 900 D84A AFS MUTANT DBREF 4M4V A 1 406 UNP Q4WQS0 Q4WQS0_ASPFU 1 406 DBREF 4M4V B 1 406 UNP Q4WQS0 Q4WQS0_ASPFU 1 406 SEQADV 4M4V HIS A -15 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS A -14 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS A -13 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS A -12 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS A -11 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS A -10 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V SER A -9 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V SER A -8 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V GLY A -7 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V LEU A -6 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V VAL A -5 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V PRO A -4 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V ARG A -3 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V GLY A -2 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V SER A -1 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS A 0 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V LEU A 171 UNP Q4WQS0 ARG 171 ENGINEERED MUTATION SEQADV 4M4V HIS B -15 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS B -14 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS B -13 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS B -12 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS B -11 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS B -10 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V SER B -9 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V SER B -8 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V GLY B -7 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V LEU B -6 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V VAL B -5 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V PRO B -4 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V ARG B -3 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V GLY B -2 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V SER B -1 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V HIS B 0 UNP Q4WQS0 EXPRESSION TAG SEQADV 4M4V LEU B 171 UNP Q4WQS0 ARG 171 ENGINEERED MUTATION SEQRES 1 A 422 HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO ARG SEQRES 2 A 422 GLY SER HIS MET GLN SER MET ARG PHE MET ILE LEU ALA SEQRES 3 A 422 LEU LEU VAL GLN PHE LEU PRO ALA TRP ALA ILE ASN ASP SEQRES 4 A 422 PRO ALA LYS SER ALA ALA PRO TYR HIS ASP GLU PHE PRO SEQRES 5 A 422 LEU PHE ARG SER ALA ASN MET ALA SER PRO ASP LYS LEU SEQRES 6 A 422 SER THR GLY ILE GLY PHE HIS SER PHE ARG ILE PRO ALA SEQRES 7 A 422 VAL VAL ARG THR THR THR GLY ARG ILE LEU ALA PHE ALA SEQRES 8 A 422 GLU GLY ARG ARG HIS THR ASN GLN ASP PHE GLY ASP ILE SEQRES 9 A 422 ASN LEU VAL TYR LYS ARG THR LYS THR THR ALA ASN ASN SEQRES 10 A 422 GLY ALA SER PRO SER ASP TRP GLU PRO LEU ARG GLU VAL SEQRES 11 A 422 VAL GLY SER GLY ALA GLY THR TRP GLY ASN PRO THR PRO SEQRES 12 A 422 VAL VAL ASP ASP ASP ASN THR ILE TYR LEU PHE LEU SER SEQRES 13 A 422 TRP ASN GLY ALA THR TYR SER GLN ASN GLY LYS ASP VAL SEQRES 14 A 422 LEU PRO ASP GLY THR VAL THR LYS LYS ILE ASP SER THR SEQRES 15 A 422 TRP GLU GLY ARG LEU HIS LEU TYR LEU THR GLU SER ARG SEQRES 16 A 422 ASP ASP GLY ASN THR TRP SER LYS PRO VAL ASP LEU THR SEQRES 17 A 422 LYS GLU LEU THR PRO ASP GLY TRP ALA TRP ASP ALA VAL SEQRES 18 A 422 GLY PRO GLY ASN GLY ILE ARG LEU THR THR GLY GLU LEU SEQRES 19 A 422 VAL ILE PRO ALA MET GLY ARG ASN ILE ILE GLY ARG GLY SEQRES 20 A 422 ALA PRO GLY ASN ARG THR TRP SER VAL GLN ARG LEU SER SEQRES 21 A 422 GLY ALA GLY ALA GLU GLY THR ILE VAL GLN THR PRO ASP SEQRES 22 A 422 GLY LYS LEU TYR ARG ASN ASP ARG PRO SER GLN LYS GLY SEQRES 23 A 422 TYR ARG MET VAL ALA ARG GLY THR LEU GLU GLY PHE GLY SEQRES 24 A 422 ALA PHE ALA PRO ASP ALA GLY LEU PRO ASP PRO ALA CYS SEQRES 25 A 422 GLN GLY SER VAL LEU ARG TYR ASN SER ASP ALA PRO ALA SEQRES 26 A 422 ARG THR ILE PHE LEU ASN SER ALA SER GLY THR SER ARG SEQRES 27 A 422 ARG ALA MET ARG VAL ARG ILE SER TYR ASP ALA ASP ALA SEQRES 28 A 422 LYS LYS PHE ASN TYR GLY ARG LYS LEU GLU ASP ALA LYS SEQRES 29 A 422 VAL SER GLY ALA GLY HIS GLU GLY GLY TYR SER SER MET SEQRES 30 A 422 THR LYS THR GLY ASP TYR LYS ILE GLY ALA LEU VAL GLU SEQRES 31 A 422 SER ASP PHE PHE ASN ASP GLY THR GLY LYS ASN SER TYR SEQRES 32 A 422 ARG ALA ILE ILE TRP ARG ARG PHE ASN LEU SER TRP ILE SEQRES 33 A 422 LEU ASN GLY PRO ASN ASN SEQRES 1 B 422 HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO ARG SEQRES 2 B 422 GLY SER HIS MET GLN SER MET ARG PHE MET ILE LEU ALA SEQRES 3 B 422 LEU LEU VAL GLN PHE LEU PRO ALA TRP ALA ILE ASN ASP SEQRES 4 B 422 PRO ALA LYS SER ALA ALA PRO TYR HIS ASP GLU PHE PRO SEQRES 5 B 422 LEU PHE ARG SER ALA ASN MET ALA SER PRO ASP LYS LEU SEQRES 6 B 422 SER THR GLY ILE GLY PHE HIS SER PHE ARG ILE PRO ALA SEQRES 7 B 422 VAL VAL ARG THR THR THR GLY ARG ILE LEU ALA PHE ALA SEQRES 8 B 422 GLU GLY ARG ARG HIS THR ASN GLN ASP PHE GLY ASP ILE SEQRES 9 B 422 ASN LEU VAL TYR LYS ARG THR LYS THR THR ALA ASN ASN SEQRES 10 B 422 GLY ALA SER PRO SER ASP TRP GLU PRO LEU ARG GLU VAL SEQRES 11 B 422 VAL GLY SER GLY ALA GLY THR TRP GLY ASN PRO THR PRO SEQRES 12 B 422 VAL VAL ASP ASP ASP ASN THR ILE TYR LEU PHE LEU SER SEQRES 13 B 422 TRP ASN GLY ALA THR TYR SER GLN ASN GLY LYS ASP VAL SEQRES 14 B 422 LEU PRO ASP GLY THR VAL THR LYS LYS ILE ASP SER THR SEQRES 15 B 422 TRP GLU GLY ARG LEU HIS LEU TYR LEU THR GLU SER ARG SEQRES 16 B 422 ASP ASP GLY ASN THR TRP SER LYS PRO VAL ASP LEU THR SEQRES 17 B 422 LYS GLU LEU THR PRO ASP GLY TRP ALA TRP ASP ALA VAL SEQRES 18 B 422 GLY PRO GLY ASN GLY ILE ARG LEU THR THR GLY GLU LEU SEQRES 19 B 422 VAL ILE PRO ALA MET GLY ARG ASN ILE ILE GLY ARG GLY SEQRES 20 B 422 ALA PRO GLY ASN ARG THR TRP SER VAL GLN ARG LEU SER SEQRES 21 B 422 GLY ALA GLY ALA GLU GLY THR ILE VAL GLN THR PRO ASP SEQRES 22 B 422 GLY LYS LEU TYR ARG ASN ASP ARG PRO SER GLN LYS GLY SEQRES 23 B 422 TYR ARG MET VAL ALA ARG GLY THR LEU GLU GLY PHE GLY SEQRES 24 B 422 ALA PHE ALA PRO ASP ALA GLY LEU PRO ASP PRO ALA CYS SEQRES 25 B 422 GLN GLY SER VAL LEU ARG TYR ASN SER ASP ALA PRO ALA SEQRES 26 B 422 ARG THR ILE PHE LEU ASN SER ALA SER GLY THR SER ARG SEQRES 27 B 422 ARG ALA MET ARG VAL ARG ILE SER TYR ASP ALA ASP ALA SEQRES 28 B 422 LYS LYS PHE ASN TYR GLY ARG LYS LEU GLU ASP ALA LYS SEQRES 29 B 422 VAL SER GLY ALA GLY HIS GLU GLY GLY TYR SER SER MET SEQRES 30 B 422 THR LYS THR GLY ASP TYR LYS ILE GLY ALA LEU VAL GLU SEQRES 31 B 422 SER ASP PHE PHE ASN ASP GLY THR GLY LYS ASN SER TYR SEQRES 32 B 422 ARG ALA ILE ILE TRP ARG ARG PHE ASN LEU SER TRP ILE SEQRES 33 B 422 LEU ASN GLY PRO ASN ASN HET DAN A 501 20 HET GOL A 502 6 HET NO3 A 503 4 HET NO3 A 504 4 HET NA A 505 1 HET GOL A 506 6 HET GOL B 501 6 HET NO3 B 502 4 HET NO3 B 503 4 HETNAM DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID HETNAM GOL GLYCEROL HETNAM NO3 NITRATE ION HETNAM NA SODIUM ION HETSYN DAN NEU5AC2EN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 DAN C11 H17 N O8 FORMUL 4 GOL 3(C3 H8 O3) FORMUL 5 NO3 4(N O3 1-) FORMUL 7 NA NA 1+ FORMUL 12 HOH *1188(H2 O) HELIX 1 1 ASP A 23 ALA A 28 5 6 HELIX 2 2 SER A 104 TRP A 108 5 5 HELIX 3 3 LEU A 191 THR A 196 1 6 HELIX 4 4 GLU A 345 LYS A 348 5 4 HELIX 5 5 ASN A 396 ASN A 402 1 7 HELIX 6 6 SER B 104 TRP B 108 5 5 HELIX 7 7 LEU B 191 THR B 196 1 6 HELIX 8 8 GLU B 345 LYS B 348 5 4 HELIX 9 9 ASN B 396 ASN B 402 1 7 SHEET 1 A 4 HIS A 32 PHE A 38 0 SHEET 2 A 4 ARG A 388 PHE A 395 -1 O ILE A 390 N LEU A 37 SHEET 3 A 4 ILE A 369 ASP A 376 -1 N ILE A 369 O PHE A 395 SHEET 4 A 4 HIS A 354 LYS A 363 -1 N GLY A 356 O GLU A 374 SHEET 1 B 4 SER A 57 ARG A 65 0 SHEET 2 B 4 ILE A 71 ARG A 78 -1 O PHE A 74 N ALA A 62 SHEET 3 B 4 ILE A 88 ARG A 94 -1 O ASN A 89 N GLY A 77 SHEET 4 B 4 ARG A 112 VAL A 115 -1 O ARG A 112 N TYR A 92 SHEET 1 C 4 GLY A 120 VAL A 129 0 SHEET 2 C 4 ILE A 135 GLY A 143 -1 O SER A 140 N GLY A 123 SHEET 3 C 4 HIS A 172 SER A 178 -1 O HIS A 172 N TRP A 141 SHEET 4 C 4 VAL A 189 ASP A 190 -1 O VAL A 189 N LEU A 175 SHEET 1 D 2 TYR A 146 SER A 147 0 SHEET 2 D 2 LYS A 161 LYS A 162 1 O LYS A 161 N SER A 147 SHEET 1 E 4 ILE A 211 ARG A 212 0 SHEET 2 E 4 LEU A 218 ALA A 222 -1 O VAL A 219 N ILE A 211 SHEET 3 E 4 ARG A 225 ARG A 230 -1 O ILE A 227 N ILE A 220 SHEET 4 E 4 THR A 237 ARG A 242 -1 O GLN A 241 N ASN A 226 SHEET 1 F 4 GLY A 250 GLN A 254 0 SHEET 2 F 4 LEU A 260 ASP A 264 -1 O ASN A 263 N THR A 251 SHEET 3 F 4 GLY A 270 THR A 278 -1 O MET A 273 N ASP A 264 SHEET 4 F 4 GLY A 281 PHE A 282 -1 O GLY A 281 N THR A 278 SHEET 1 G 4 GLY A 250 GLN A 254 0 SHEET 2 G 4 LEU A 260 ASP A 264 -1 O ASN A 263 N THR A 251 SHEET 3 G 4 GLY A 270 THR A 278 -1 O MET A 273 N ASP A 264 SHEET 4 G 4 ALA A 286 ASP A 293 -1 O ASP A 293 N GLY A 270 SHEET 1 H 4 SER A 299 ASN A 304 0 SHEET 2 H 4 ARG A 310 SER A 316 -1 O ILE A 312 N LEU A 301 SHEET 3 H 4 MET A 325 SER A 330 -1 O SER A 330 N THR A 311 SHEET 4 H 4 ARG A 342 LYS A 343 -1 O ARG A 342 N VAL A 327 SHEET 1 I 4 HIS B 32 PHE B 38 0 SHEET 2 I 4 ARG B 388 PHE B 395 -1 O ILE B 390 N LEU B 37 SHEET 3 I 4 ILE B 369 ASP B 376 -1 N VAL B 373 O ILE B 391 SHEET 4 I 4 HIS B 354 LYS B 363 -1 N THR B 362 O GLY B 370 SHEET 1 J 4 SER B 57 ARG B 65 0 SHEET 2 J 4 ILE B 71 ARG B 78 -1 O PHE B 74 N ALA B 62 SHEET 3 J 4 ILE B 88 ARG B 94 -1 O LYS B 93 N ALA B 73 SHEET 4 J 4 ARG B 112 VAL B 115 -1 O ARG B 112 N TYR B 92 SHEET 1 K 4 GLY B 120 VAL B 129 0 SHEET 2 K 4 ILE B 135 GLY B 143 -1 O TYR B 136 N VAL B 128 SHEET 3 K 4 HIS B 172 SER B 178 -1 O HIS B 172 N TRP B 141 SHEET 4 K 4 VAL B 189 ASP B 190 -1 O VAL B 189 N LEU B 175 SHEET 1 L 2 TYR B 146 SER B 147 0 SHEET 2 L 2 LYS B 161 LYS B 162 1 O LYS B 161 N SER B 147 SHEET 1 M 4 ILE B 211 ARG B 212 0 SHEET 2 M 4 LEU B 218 ALA B 222 -1 O VAL B 219 N ILE B 211 SHEET 3 M 4 ARG B 225 ARG B 230 -1 O ILE B 227 N ILE B 220 SHEET 4 M 4 THR B 237 ARG B 242 -1 O GLN B 241 N ASN B 226 SHEET 1 N 4 GLY B 250 GLN B 254 0 SHEET 2 N 4 LEU B 260 ASP B 264 -1 O ASN B 263 N THR B 251 SHEET 3 N 4 GLY B 270 THR B 278 -1 O MET B 273 N ASP B 264 SHEET 4 N 4 GLY B 281 PHE B 282 -1 O GLY B 281 N THR B 278 SHEET 1 O 4 GLY B 250 GLN B 254 0 SHEET 2 O 4 LEU B 260 ASP B 264 -1 O ASN B 263 N THR B 251 SHEET 3 O 4 GLY B 270 THR B 278 -1 O MET B 273 N ASP B 264 SHEET 4 O 4 ALA B 286 ASP B 293 -1 O ASP B 293 N GLY B 270 SHEET 1 P 4 SER B 299 ASN B 304 0 SHEET 2 P 4 ARG B 310 SER B 316 -1 O ILE B 312 N LEU B 301 SHEET 3 P 4 MET B 325 SER B 330 -1 O ARG B 326 N ASN B 315 SHEET 4 P 4 ARG B 342 LYS B 343 -1 O ARG B 342 N VAL B 327 LINK OD1 ASP A 87 NA NA A 505 1555 1555 2.74 LINK O ILE A 88 NA NA A 505 1555 1555 2.43 LINK OD1 ASN A 89 NA NA A 505 1555 1555 2.56 LINK O ASER A 117 NA NA A 505 1555 1555 2.51 LINK O GLY A 120 NA NA A 505 1555 1555 2.28 CISPEP 1 GLY A 206 PRO A 207 0 4.34 CISPEP 2 ALA A 307 PRO A 308 0 -8.25 CISPEP 3 GLY B 206 PRO B 207 0 3.90 CISPEP 4 ALA B 307 PRO B 308 0 -5.45 CRYST1 75.880 57.970 94.640 90.00 99.89 90.00 P 1 21 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 0.013179 0.000000 0.002298 0.00000 SCALE2 0.000000 0.017250 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010726 0.00000