HEADER LYASE 25-FEB-21 7NNK TITLE CRYSTAL STRUCTURE OF S116A MUTANT OF HYDROXY KETONE ALDOLASE (SWHKA) TITLE 2 FROM SPHINGOMONAS WITTICHII RW1 IN COMPLEX WITH HYDROXYPYRUVATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HPCH/HPAI ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HYDROXY KETOACID ALDOLASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPHINGOMONAS WITTICHII (STRAIN RW1 / DSM 6014 / SOURCE 3 JCM 10273); SOURCE 4 ORGANISM_TAXID: 392499; SOURCE 5 STRAIN: RW1 / DSM 6014 / JCM 10273; SOURCE 6 GENE: SWIT_5035; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CLASS II PYRUVATE ALDOLASE, METAL DEPENDENT, ALDOL REACTION, KEYWDS 2 HYDROXYPYRUVATE, PYRUVATE, ALDOLASE, CLASS II, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR I.JUSTO,S.R.MARSDEN,U.HANEFELD,I.BENTO REVDAT 4 31-JAN-24 7NNK 1 REMARK REVDAT 3 07-DEC-22 7NNK 1 JRNL REVDAT 2 23-NOV-22 7NNK 1 JRNL REVDAT 1 16-NOV-22 7NNK 0 JRNL AUTH S.R.MARSDEN,H.J.WIJMA,M.K.F.MOHR,I.JUSTO,P.L.HAGEDOORN, JRNL AUTH 2 J.LAUSTSEN,C.M.JEFFRIES,D.SVERGUN,L.MESTROM,D.G.G.MCMILLAN, JRNL AUTH 3 I.BENTO,U.HANEFELD JRNL TITL SUBSTRATE INDUCED MOVEMENT OF THE METAL COFACTOR BETWEEN JRNL TITL 2 ACTIVE AND RESTING STATE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 61 13338 2022 JRNL REFN ESSN 1521-3773 JRNL PMID 36214476 JRNL DOI 10.1002/ANIE.202213338 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 38701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.002 REMARK 3 FREE R VALUE TEST SET COUNT : 1936 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2706 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3731 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 299 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16500 REMARK 3 B22 (A**2) : -0.16500 REMARK 3 B33 (A**2) : 0.53600 REMARK 3 B12 (A**2) : -0.08300 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): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.708 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3886 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3700 ; 0.003 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5282 ; 1.666 ; 1.633 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8488 ; 1.343 ; 1.574 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 517 ; 6.954 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;29.644 ;21.005 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 592 ;12.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;14.454 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 516 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4508 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 874 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 702 ; 0.184 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 116 ; 0.122 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1842 ; 0.142 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 235 ; 0.140 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.002 ; 0.200 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): 2038 ; 1.529 ; 2.216 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2036 ; 1.525 ; 2.217 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2553 ; 2.113 ; 3.317 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2554 ; 2.112 ; 3.317 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1848 ; 2.083 ; 2.440 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1843 ; 2.074 ; 2.440 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2725 ; 3.139 ; 3.575 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2726 ; 3.138 ; 3.574 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 BULK SOLVENT 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: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7NNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-20 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 : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : OXFORD-FNB REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38705 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 74.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 9.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 74.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.02600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6R62 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, HEPES, MAGNESIUM CHLORIDE, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.66350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.59033 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.39500 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 35.66350 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 20.59033 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 74.39500 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 35.66350 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 20.59033 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 74.39500 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.18066 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 148.79000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 41.18066 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 148.79000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 41.18066 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 148.79000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -209.0 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 454 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 534 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 559 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 562 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 563 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 564 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 533 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 ALA A 250 REMARK 465 LEU A 251 REMARK 465 GLY B 11 REMARK 465 SER B 128 REMARK 465 LEU B 251 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 HIS A 0 CG ND1 CD2 CE1 NE2 REMARK 480 HIS B 0 CB CG ND1 CD2 CE1 NE2 REMARK 480 ARG B 12 NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 412 O HOH B 441 2.18 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 HIS A 0 CB HIS A 0 CG -0.144 REMARK 500 ARG B 12 CD ARG B 12 NE -0.136 REMARK 500 GLU B 155 CD GLU B 155 OE1 0.077 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 GLN A 43 -61.44 -91.52 REMARK 500 HIS A 44 55.22 -111.17 REMARK 500 HIS B 44 58.76 -119.91 REMARK 500 GLU B 145 24.69 -153.49 REMARK 500 ASP B 160 -93.25 -56.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP B 160 11.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 564 DISTANCE = 6.18 ANGSTROMS 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 145 OE1 REMARK 620 2 ASP A 171 OD2 93.9 REMARK 620 3 3PY A 301 O1 94.8 93.8 REMARK 620 4 3PY A 301 O3 101.7 160.8 73.9 REMARK 620 5 HOH A 430 O 172.2 87.3 92.8 78.8 REMARK 620 6 HOH A 463 O 83.3 99.0 167.2 94.0 88.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 145 OE1 REMARK 620 2 ASP B 171 OD2 89.7 REMARK 620 3 HOH B 412 O 86.9 116.5 REMARK 620 4 HOH B 441 O 81.1 65.5 51.3 REMARK 620 5 HOH B 483 O 173.9 93.7 87.1 95.7 REMARK 620 6 HOH B 501 O 92.3 91.8 151.7 156.2 92.6 REMARK 620 7 HOH B 509 O 106.6 151.5 88.2 138.9 72.4 64.9 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6R62 RELATED DB: PDB REMARK 900 6R62 CONTAINS THE NATIVE PROTEIN COMPLEXED WITH HYDROXYPYRUVATE DBREF 7NNK A 2 251 UNP A5VH82 A5VH82_SPHWW 2 251 DBREF 7NNK B 2 251 UNP A5VH82 A5VH82_SPHWW 2 251 SEQADV 7NNK HIS A 0 UNP A5VH82 EXPRESSION TAG SEQADV 7NNK HIS A 1 UNP A5VH82 EXPRESSION TAG SEQADV 7NNK ALA A 116 UNP A5VH82 SER 116 ENGINEERED MUTATION SEQADV 7NNK HIS B 0 UNP A5VH82 EXPRESSION TAG SEQADV 7NNK HIS B 1 UNP A5VH82 EXPRESSION TAG SEQADV 7NNK ALA B 116 UNP A5VH82 SER 116 ENGINEERED MUTATION SEQRES 1 A 252 HIS HIS ASN LYS VAL ARG THR CYS TRP ASN GLU GLY ARG SEQRES 2 A 252 PRO ALA LEU ALA GLY TRP LEU GLN LEU PRO GLY THR LEU SEQRES 3 A 252 HIS ALA GLU ALA LEU ALA ARG LEU ASP TYR ASP ALA VAL SEQRES 4 A 252 VAL ILE ASP MET GLN HIS SER PRO ILE ASP PHE GLY GLN SEQRES 5 A 252 VAL ALA PRO MET LEU ILE ALA ILE GLU LEU GLY GLY ALA SEQRES 6 A 252 GLU PRO PHE VAL ARG THR GLN VAL ASN ASP PRO SER ASP SEQRES 7 A 252 ILE MET LYS LEU LEU ASP ALA GLY ALA TYR GLY ILE ILE SEQRES 8 A 252 ALA PRO MET VAL ASN THR ARG ALA GLU ALA GLN THR LEU SEQRES 9 A 252 ALA SER ALA LEU HIS TYR SER PRO ARG GLY LEU ARG ALA SEQRES 10 A 252 PHE GLY PRO ARG ARG PRO SER LEU ARG TYR GLY SER GLY SEQRES 11 A 252 TYR LEU ALA GLN ALA SER GLU THR VAL VAL GLY LEU ALA SEQRES 12 A 252 MET ILE GLU THR ARG GLU ALA LEU ALA ASN ILE ASP GLU SEQRES 13 A 252 ILE LEU SER VAL ASP GLY ILE ASP GLY VAL PHE ILE GLY SEQRES 14 A 252 PRO THR ASP LEU ALA LEU ASP LEU GLY HIS ALA PRO LEU SEQRES 15 A 252 VAL ASP THR GLU GLU ALA GLU VAL VAL SER ALA ILE ALA SEQRES 16 A 252 HIS VAL ARG GLU ARG ALA HIS ALA ALA GLY LYS ARG VAL SEQRES 17 A 252 GLY ILE PHE CYS GLY SER GLY GLY PHE ALA ARG VAL LYS SEQRES 18 A 252 LEU ALA GLU GLY PHE ASP PHE VAL THR ALA ALA PRO ASP SEQRES 19 A 252 LEU ALA MET LEU SER ALA ALA ALA ARG GLN VAL ILE ALA SEQRES 20 A 252 ASP ALA ARG ALA LEU SEQRES 1 B 252 HIS HIS ASN LYS VAL ARG THR CYS TRP ASN GLU GLY ARG SEQRES 2 B 252 PRO ALA LEU ALA GLY TRP LEU GLN LEU PRO GLY THR LEU SEQRES 3 B 252 HIS ALA GLU ALA LEU ALA ARG LEU ASP TYR ASP ALA VAL SEQRES 4 B 252 VAL ILE ASP MET GLN HIS SER PRO ILE ASP PHE GLY GLN SEQRES 5 B 252 VAL ALA PRO MET LEU ILE ALA ILE GLU LEU GLY GLY ALA SEQRES 6 B 252 GLU PRO PHE VAL ARG THR GLN VAL ASN ASP PRO SER ASP SEQRES 7 B 252 ILE MET LYS LEU LEU ASP ALA GLY ALA TYR GLY ILE ILE SEQRES 8 B 252 ALA PRO MET VAL ASN THR ARG ALA GLU ALA GLN THR LEU SEQRES 9 B 252 ALA SER ALA LEU HIS TYR SER PRO ARG GLY LEU ARG ALA SEQRES 10 B 252 PHE GLY PRO ARG ARG PRO SER LEU ARG TYR GLY SER GLY SEQRES 11 B 252 TYR LEU ALA GLN ALA SER GLU THR VAL VAL GLY LEU ALA SEQRES 12 B 252 MET ILE GLU THR ARG GLU ALA LEU ALA ASN ILE ASP GLU SEQRES 13 B 252 ILE LEU SER VAL ASP GLY ILE ASP GLY VAL PHE ILE GLY SEQRES 14 B 252 PRO THR ASP LEU ALA LEU ASP LEU GLY HIS ALA PRO LEU SEQRES 15 B 252 VAL ASP THR GLU GLU ALA GLU VAL VAL SER ALA ILE ALA SEQRES 16 B 252 HIS VAL ARG GLU ARG ALA HIS ALA ALA GLY LYS ARG VAL SEQRES 17 B 252 GLY ILE PHE CYS GLY SER GLY GLY PHE ALA ARG VAL LYS SEQRES 18 B 252 LEU ALA GLU GLY PHE ASP PHE VAL THR ALA ALA PRO ASP SEQRES 19 B 252 LEU ALA MET LEU SER ALA ALA ALA ARG GLN VAL ILE ALA SEQRES 20 B 252 ASP ALA ARG ALA LEU HET 3PY A 301 10 HET MG A 302 1 HET MG B 301 1 HETNAM 3PY 3-HYDROXYPYRUVIC ACID HETNAM MG MAGNESIUM ION FORMUL 3 3PY C3 H4 O4 FORMUL 4 MG 2(MG 2+) FORMUL 6 HOH *299(H2 O) HELIX 1 AA1 ASN A 2 GLU A 10 1 9 HELIX 2 AA2 THR A 24 LEU A 33 1 10 HELIX 3 AA3 ASP A 48 GLY A 63 1 16 HELIX 4 AA4 ASP A 74 ALA A 84 1 11 HELIX 5 AA5 THR A 96 HIS A 108 1 13 HELIX 6 AA6 PRO A 119 GLY A 127 1 9 HELIX 7 AA7 GLY A 129 VAL A 138 1 10 HELIX 8 AA8 THR A 146 ASN A 152 1 7 HELIX 9 AA9 ASN A 152 SER A 158 1 7 HELIX 10 AB1 GLY A 168 LEU A 176 1 9 HELIX 11 AB2 GLU A 186 ALA A 203 1 18 HELIX 12 AB3 SER A 213 GLY A 224 1 12 HELIX 13 AB4 ASP A 233 ARG A 249 1 17 HELIX 14 AB5 ASN B 2 GLU B 10 1 9 HELIX 15 AB6 THR B 24 ARG B 32 1 9 HELIX 16 AB7 ASP B 48 GLY B 63 1 16 HELIX 17 AB8 ASP B 74 ALA B 84 1 11 HELIX 18 AB9 THR B 96 HIS B 108 1 13 HELIX 19 AC1 PRO B 119 GLY B 127 1 9 HELIX 20 AC2 TYR B 130 ALA B 134 1 5 HELIX 21 AC3 SER B 135 VAL B 138 5 4 HELIX 22 AC4 THR B 146 ASN B 152 1 7 HELIX 23 AC5 ASN B 152 SER B 158 1 7 HELIX 24 AC6 GLY B 168 LEU B 176 1 9 HELIX 25 AC7 GLU B 186 ALA B 203 1 18 HELIX 26 AC8 SER B 213 GLU B 223 1 11 HELIX 27 AC9 ASP B 233 ALA B 250 1 18 SHEET 1 AA1 9 ALA A 14 LEU A 19 0 SHEET 2 AA1 9 ALA A 37 ASP A 41 1 O ASP A 41 N LEU A 19 SHEET 3 AA1 9 GLU A 65 ARG A 69 1 O PHE A 67 N ILE A 40 SHEET 4 AA1 9 GLY A 88 ALA A 91 1 O ILE A 90 N VAL A 68 SHEET 5 AA1 9 VAL A 139 ILE A 144 1 O LEU A 141 N ILE A 89 SHEET 6 AA1 9 GLY A 164 ILE A 167 1 O GLY A 164 N ALA A 142 SHEET 7 AA1 9 ARG A 206 PHE A 210 1 O GLY A 208 N ILE A 167 SHEET 8 AA1 9 PHE A 227 PRO A 232 1 O THR A 229 N ILE A 209 SHEET 9 AA1 9 ALA A 14 LEU A 19 1 N ALA A 16 O VAL A 228 SHEET 1 AA2 9 ALA B 14 LEU B 19 0 SHEET 2 AA2 9 ALA B 37 ASP B 41 1 O ASP B 41 N LEU B 19 SHEET 3 AA2 9 GLU B 65 ARG B 69 1 O PHE B 67 N VAL B 38 SHEET 4 AA2 9 GLY B 88 ALA B 91 1 O ILE B 90 N VAL B 68 SHEET 5 AA2 9 VAL B 139 ILE B 144 1 O LEU B 141 N ILE B 89 SHEET 6 AA2 9 GLY B 164 ILE B 167 1 O GLY B 164 N ALA B 142 SHEET 7 AA2 9 ARG B 206 PHE B 210 1 O GLY B 208 N ILE B 167 SHEET 8 AA2 9 PHE B 227 PRO B 232 1 O THR B 229 N ILE B 209 SHEET 9 AA2 9 ALA B 14 LEU B 19 1 N ALA B 16 O VAL B 228 LINK OE1 GLU A 145 MG MG A 302 1555 1555 2.09 LINK OD2 ASP A 171 MG MG A 302 1555 1555 2.05 LINK O1 3PY A 301 MG MG A 302 1555 1555 2.07 LINK O3 3PY A 301 MG MG A 302 1555 1555 2.06 LINK MG MG A 302 O HOH A 430 1555 1555 2.11 LINK MG MG A 302 O HOH A 463 1555 1555 2.08 LINK OE1 GLU B 145 MG MG B 301 1555 1555 2.11 LINK OD2 ASP B 171 MG MG B 301 1555 1555 2.06 LINK MG MG B 301 O HOH B 412 1555 1555 2.05 LINK MG MG B 301 O HOH B 441 1555 1555 2.76 LINK MG MG B 301 O HOH B 483 1555 1555 2.09 LINK MG MG B 301 O HOH B 501 1555 1555 2.08 LINK MG MG B 301 O HOH B 509 1555 1555 2.08 CISPEP 1 SER A 110 PRO A 111 0 6.11 CISPEP 2 ALA A 230 ALA A 231 0 -23.47 CISPEP 3 SER B 110 PRO B 111 0 12.26 CISPEP 4 ALA B 230 ALA B 231 0 -15.60 CRYST1 71.327 71.327 223.185 90.00 90.00 120.00 H 3 18 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 0.014020 0.008094 0.000000 0.00000 SCALE2 0.000000 0.016189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004481 0.00000