HEADER LYASE 03-DEC-15 5FQ0 TITLE THE STRUCTURE OF KDGF FROM HALOMONAS SP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: KDGF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: KDGF; COMPND 7 CHAIN: B, C, D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: RESIDUAL CLEAVED HIS TAG; COMPND 11 CHAIN: H; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOMONAS SP.; SOURCE 3 ORGANISM_TAXID: 1486246; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A-HAKDGF; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HALOMONAS SP.; SOURCE 11 ORGANISM_TAXID: 1486246; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET28A-HAKDGF; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HALOMONAS SP.; SOURCE 19 ORGANISM_TAXID: 1486246; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 22 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 23 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PET28A-HAKDGF KEYWDS LYASE, KDGF, PECTIN, ALGINATE, URONATE SUGAR METABOLISM, CUPIN EXPDTA X-RAY DIFFRACTION AUTHOR J.K.HOBBS,S.M.LEE,M.ROBB,F.HOF,C.BARR,K.T.ABE,J.H.HEHEMANN,R.MCLEAN, AUTHOR 2 D.W.ABBOTT,A.B.BORASTON REVDAT 4 10-JAN-24 5FQ0 1 REMARK LINK REVDAT 3 15-JUN-16 5FQ0 1 JRNL REVDAT 2 01-JUN-16 5FQ0 1 JRNL REVDAT 1 04-MAY-16 5FQ0 0 JRNL AUTH J.K.HOBBS,S.M.LEE,M.ROBB,F.HOF,C.BARR,K.T.ABE,J.HEHEMANN, JRNL AUTH 2 R.MCLEAN,D.W.ABBOTT,A.B.BORASTON JRNL TITL KDGF, THE MISSING LINK IN THE MICROBIAL METABOLISM OF JRNL TITL 2 URONATE SUGARS FROM PECTIN AND ALGINATE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 6188 2016 JRNL REFN ISSN 0027-8424 JRNL PMID 27185956 JRNL DOI 10.1073/PNAS.1524214113 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34364 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1810 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2502 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 140 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 281 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : 2.34000 REMARK 3 B33 (A**2) : -1.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.412 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3620 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4911 ; 1.777 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 436 ; 7.413 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;32.198 ;23.472 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 553 ;15.243 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;21.527 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 515 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2869 ; 0.008 ; 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): 1753 ; 1.897 ; 2.751 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2183 ; 2.725 ; 4.102 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1867 ; 2.877 ; 3.074 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5396 ; 6.289 ;24.094 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 5FQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1290065703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22373 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 5FPX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 55.46700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.34000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 55.46700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.34000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.6 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: 3 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: H 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 ASN A 2 REMARK 465 LYS A 113 REMARK 465 SER A 114 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 THR B 3 REMARK 465 LYS B 113 REMARK 465 SER B 114 REMARK 465 MET C 1 REMARK 465 ASN C 2 REMARK 465 THR C 3 REMARK 465 GLY C 4 REMARK 465 SER C 114 REMARK 465 MET D 1 REMARK 465 ASN D 2 REMARK 465 THR D 3 REMARK 465 GLY D 4 REMARK 465 LYS D 113 REMARK 465 SER D 114 REMARK 465 HIS H 4 REMARK 465 HIS H 5 REMARK 465 HIS H 6 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU C 51 CG CD OE1 OE2 REMARK 470 LYS C 113 CG CD CE NZ REMARK 470 GLU D 51 CG CD OE1 OE2 REMARK 470 GLU D 71 CG CD OE1 OE2 REMARK 470 LYS D 72 CG CD CE NZ 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 H 2001 O HOH H 2002 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU A 103 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 LEU A 103 CB - CG - CD2 ANGL. DEV. = -16.6 DEGREES REMARK 500 LEU C 103 CA - CB - CG ANGL. DEV. = 22.6 DEGREES REMARK 500 LEU C 103 CB - CG - CD2 ANGL. DEV. = -12.2 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 PRO A 106 -165.87 -73.29 REMARK 500 VAL B 17 -63.78 -102.34 REMARK 500 PRO B 106 -164.58 -74.81 REMARK 500 PRO C 106 -161.16 -78.34 REMARK 500 GLU D 69 60.68 38.77 REMARK 500 PRO D 106 -168.81 -71.03 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 NI A1113 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 48 NE2 REMARK 620 2 HIS A 50 NE2 95.3 REMARK 620 3 GLN A 55 OE1 174.5 88.2 REMARK 620 4 HIS A 89 NE2 87.5 103.2 87.6 REMARK 620 5 FLC A1114 CGC 86.5 119.1 95.5 137.7 REMARK 620 6 FLC A1114 OG1 93.7 87.5 90.8 169.1 31.8 REMARK 620 7 FLC A1114 OG2 88.0 150.7 91.1 106.0 31.9 63.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1113 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 48 NE2 REMARK 620 2 HIS B 50 NE2 93.1 REMARK 620 3 GLN B 55 OE1 171.3 92.4 REMARK 620 4 HIS B 89 NE2 89.8 107.1 82.2 REMARK 620 5 FLC B1114 CGC 83.7 118.8 99.6 133.9 REMARK 620 6 FLC B1114 OG1 89.3 87.2 97.7 165.7 31.9 REMARK 620 7 FLC B1114 OG2 86.0 150.0 92.6 102.9 31.3 62.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C1114 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 48 NE2 REMARK 620 2 HIS C 50 NE2 102.0 REMARK 620 3 GLN C 55 OE1 171.5 84.7 REMARK 620 4 HIS C 89 NE2 89.0 100.2 84.7 REMARK 620 5 FLC C1115 OG2 82.1 155.0 93.9 104.5 REMARK 620 6 FLC C1115 OG1 91.9 90.8 93.1 168.5 64.3 REMARK 620 7 FLC C1115 CGC 82.4 123.1 98.3 136.6 32.3 32.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI D1113 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 48 NE2 REMARK 620 2 HIS D 50 NE2 96.4 REMARK 620 3 GLN D 55 OE1 173.0 90.3 REMARK 620 4 HIS D 89 NE2 89.3 103.5 90.9 REMARK 620 5 FLC D1114 OG2 81.0 149.2 92.2 107.2 REMARK 620 6 FLC D1114 OG1 87.6 89.4 90.7 167.0 59.9 REMARK 620 7 FLC D1114 CGC 77.4 119.3 97.7 136.1 30.0 31.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI H1004 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS H 1 ND1 REMARK 620 2 HIS H 2 ND1 139.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI D 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1113 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC A 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC B 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC C 1115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC D 1114 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI H 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FPX RELATED DB: PDB REMARK 900 THE STRUCTURE OF KDGF FROM YERSINIA ENTEROCOLITICA. REMARK 900 RELATED ID: 5FPZ RELATED DB: PDB REMARK 900 THE STRUCTURE OF KDGF FROM YERSINIA ENTEROCOLITICA WITH CITRATE REMARK 900 BOUND IN THE ACTIVE SITE. DBREF 5FQ0 A 1 114 PDB 5FQ0 5FQ0 1 114 DBREF 5FQ0 B 1 114 PDB 5FQ0 5FQ0 1 114 DBREF 5FQ0 C 1 114 PDB 5FQ0 5FQ0 1 114 DBREF 5FQ0 D 1 114 PDB 5FQ0 5FQ0 1 114 DBREF 5FQ0 H 1 6 PDB 5FQ0 5FQ0 1 6 SEQRES 1 A 114 MET ASN THR GLY SER PHE PHE ILE ASN HIS GLU HIS ASP SEQRES 2 A 114 TRP GLN ASP VAL GLU PRO GLY ILE GLN ARG LYS ILE VAL SEQRES 3 A 114 ALA HIS THR PRO ASP LEU MET ALA VAL CYS VAL LYS PHE SEQRES 4 A 114 ASP ARG GLY ALA VAL GLY THR PRO HIS GLN HIS GLU ARG SEQRES 5 A 114 HIS ASP GLN ILE GLY TYR VAL VAL GLN GLY ALA PHE GLU SEQRES 6 A 114 VAL GLU LEU GLU GLY GLU LYS ARG ARG LEU SER PRO GLY SEQRES 7 A 114 ASP ALA PHE VAL ALA PRO HIS HIS THR MET HIS GLY ALA SEQRES 8 A 114 VAL ALA LEU GLU PRO ASP SER LEU VAL ILE ASP LEU PHE SEQRES 9 A 114 SER PRO ARG ARG ASP ASP MET LEU LYS SER SEQRES 1 B 114 MET ASN THR GLY SER PHE PHE ILE ASN ASP GLU HIS ASP SEQRES 2 B 114 TRP GLN ASP VAL GLU PRO GLY ILE GLN ARG LYS ILE VAL SEQRES 3 B 114 ALA HIS THR PRO ASP LEU MET ALA VAL CYS VAL LYS PHE SEQRES 4 B 114 ASP ARG GLY ALA VAL GLY THR PRO HIS GLN HIS GLU ARG SEQRES 5 B 114 HIS ASP GLN ILE GLY TYR VAL VAL GLN GLY ALA PHE GLU SEQRES 6 B 114 VAL GLU LEU GLU GLY GLU LYS ARG ARG LEU SER PRO GLY SEQRES 7 B 114 ASP ALA PHE VAL ALA PRO HIS HIS THR MET HIS GLY ALA SEQRES 8 B 114 VAL ALA LEU GLU PRO ASP SER LEU VAL ILE ASP LEU PHE SEQRES 9 B 114 SER PRO ARG ARG ASP ASP MET LEU LYS SER SEQRES 1 C 114 MET ASN THR GLY SER PHE PHE ILE ASN ASP GLU HIS ASP SEQRES 2 C 114 TRP GLN ASP VAL GLU PRO GLY ILE GLN ARG LYS ILE VAL SEQRES 3 C 114 ALA HIS THR PRO ASP LEU MET ALA VAL CYS VAL LYS PHE SEQRES 4 C 114 ASP ARG GLY ALA VAL GLY THR PRO HIS GLN HIS GLU ARG SEQRES 5 C 114 HIS ASP GLN ILE GLY TYR VAL VAL GLN GLY ALA PHE GLU SEQRES 6 C 114 VAL GLU LEU GLU GLY GLU LYS ARG ARG LEU SER PRO GLY SEQRES 7 C 114 ASP ALA PHE VAL ALA PRO HIS HIS THR MET HIS GLY ALA SEQRES 8 C 114 VAL ALA LEU GLU PRO ASP SER LEU VAL ILE ASP LEU PHE SEQRES 9 C 114 SER PRO ARG ARG ASP ASP MET LEU LYS SER SEQRES 1 D 114 MET ASN THR GLY SER PHE PHE ILE ASN ASP GLU HIS ASP SEQRES 2 D 114 TRP GLN ASP VAL GLU PRO GLY ILE GLN ARG LYS ILE VAL SEQRES 3 D 114 ALA HIS THR PRO ASP LEU MET ALA VAL CYS VAL LYS PHE SEQRES 4 D 114 ASP ARG GLY ALA VAL GLY THR PRO HIS GLN HIS GLU ARG SEQRES 5 D 114 HIS ASP GLN ILE GLY TYR VAL VAL GLN GLY ALA PHE GLU SEQRES 6 D 114 VAL GLU LEU GLU GLY GLU LYS ARG ARG LEU SER PRO GLY SEQRES 7 D 114 ASP ALA PHE VAL ALA PRO HIS HIS THR MET HIS GLY ALA SEQRES 8 D 114 VAL ALA LEU GLU PRO ASP SER LEU VAL ILE ASP LEU PHE SEQRES 9 D 114 SER PRO ARG ARG ASP ASP MET LEU LYS SER SEQRES 1 H 6 HIS HIS HIS HIS HIS HIS HET NI A1113 1 HET FLC A1114 13 HET NI B1113 1 HET FLC B1114 13 HET NI C1114 1 HET FLC C1115 13 HET NI D1113 1 HET FLC D1114 13 HET NI H1004 1 HETNAM NI NICKEL (II) ION HETNAM FLC CITRATE ANION FORMUL 6 NI 5(NI 2+) FORMUL 7 FLC 4(C6 H5 O7 3-) FORMUL 15 HOH *281(H2 O) HELIX 1 1 ILE A 8 HIS A 12 5 5 HELIX 2 2 ARG A 108 LEU A 112 5 5 HELIX 3 3 ILE B 8 HIS B 12 5 5 HELIX 4 4 ARG B 108 LEU B 112 5 5 HELIX 5 5 ILE C 8 HIS C 12 5 5 HELIX 6 6 ARG C 108 LEU C 112 5 5 HELIX 7 7 ILE D 8 HIS D 12 5 5 HELIX 8 8 ARG D 108 LEU D 112 5 5 SHEET 1 AA 7 SER A 5 PHE A 7 0 SHEET 2 AA 7 ALA B 80 ALA B 83 -1 O ALA B 80 N PHE A 7 SHEET 3 AA 7 ASP B 54 GLN B 61 -1 O GLN B 55 N ALA B 83 SHEET 4 AA 7 SER B 98 SER B 105 -1 O LEU B 99 N VAL B 60 SHEET 5 AA 7 LEU B 32 PHE B 39 -1 O MET B 33 N PHE B 104 SHEET 6 AA 7 ILE B 21 THR B 29 -1 O GLN B 22 N LYS B 38 SHEET 7 AA 7 GLN B 15 GLU B 18 -1 O GLN B 15 N ARG B 23 SHEET 1 AB 7 GLN A 15 GLU A 18 0 SHEET 2 AB 7 ILE A 21 THR A 29 -1 O ILE A 21 N VAL A 17 SHEET 3 AB 7 LEU A 32 PHE A 39 -1 O LEU A 32 N THR A 29 SHEET 4 AB 7 SER A 98 SER A 105 -1 O SER A 98 N PHE A 39 SHEET 5 AB 7 ASP A 54 GLN A 61 -1 O ASP A 54 N SER A 105 SHEET 6 AB 7 ALA A 80 ALA A 83 -1 O PHE A 81 N GLY A 57 SHEET 7 AB 7 SER B 5 PHE B 7 -1 O SER B 5 N VAL A 82 SHEET 1 AC 4 VAL A 44 HIS A 48 0 SHEET 2 AC 4 HIS A 89 ALA A 93 -1 O HIS A 89 N HIS A 48 SHEET 3 AC 4 PHE A 64 LEU A 68 -1 O GLU A 65 N VAL A 92 SHEET 4 AC 4 GLU A 71 LEU A 75 -1 O GLU A 71 N LEU A 68 SHEET 1 BA 4 VAL B 44 HIS B 48 0 SHEET 2 BA 4 HIS B 89 ALA B 93 -1 O HIS B 89 N HIS B 48 SHEET 3 BA 4 PHE B 64 LEU B 68 -1 O GLU B 65 N VAL B 92 SHEET 4 BA 4 GLU B 71 LEU B 75 -1 O GLU B 71 N LEU B 68 SHEET 1 CA 7 PHE C 6 PHE C 7 0 SHEET 2 CA 7 ALA D 80 ALA D 83 -1 O ALA D 80 N PHE C 7 SHEET 3 CA 7 ASP D 54 GLN D 61 -1 O GLN D 55 N ALA D 83 SHEET 4 CA 7 SER D 98 SER D 105 -1 O LEU D 99 N VAL D 60 SHEET 5 CA 7 LEU D 32 PHE D 39 -1 O MET D 33 N PHE D 104 SHEET 6 CA 7 ILE D 21 THR D 29 -1 O GLN D 22 N LYS D 38 SHEET 7 CA 7 GLN D 15 GLU D 18 -1 O GLN D 15 N ARG D 23 SHEET 1 CB 7 GLN C 15 GLU C 18 0 SHEET 2 CB 7 ILE C 21 THR C 29 -1 O ILE C 21 N VAL C 17 SHEET 3 CB 7 LEU C 32 PHE C 39 -1 O LEU C 32 N THR C 29 SHEET 4 CB 7 SER C 98 SER C 105 -1 O SER C 98 N PHE C 39 SHEET 5 CB 7 ASP C 54 GLN C 61 -1 O ASP C 54 N SER C 105 SHEET 6 CB 7 ALA C 80 ALA C 83 -1 O PHE C 81 N GLY C 57 SHEET 7 CB 7 PHE D 6 PHE D 7 -1 O PHE D 7 N ALA C 80 SHEET 1 CC 4 VAL C 44 HIS C 48 0 SHEET 2 CC 4 HIS C 89 ALA C 93 -1 O HIS C 89 N HIS C 48 SHEET 3 CC 4 PHE C 64 LEU C 68 -1 O GLU C 65 N VAL C 92 SHEET 4 CC 4 GLU C 71 LEU C 75 -1 O GLU C 71 N LEU C 68 SHEET 1 DA 4 VAL D 44 HIS D 48 0 SHEET 2 DA 4 HIS D 89 ALA D 93 -1 O HIS D 89 N HIS D 48 SHEET 3 DA 4 PHE D 64 LEU D 68 -1 O GLU D 65 N VAL D 92 SHEET 4 DA 4 GLU D 71 LEU D 75 -1 O GLU D 71 N LEU D 68 LINK NE2 HIS A 48 NI NI A1113 1555 1555 2.15 LINK NE2 HIS A 50 NI NI A1113 1555 1555 2.05 LINK OE1 GLN A 55 NI NI A1113 1555 1555 2.14 LINK NE2 HIS A 89 NI NI A1113 1555 1555 2.12 LINK NI NI A1113 CGC FLC A1114 1555 1555 2.42 LINK NI NI A1113 OG1 FLC A1114 1555 1555 2.05 LINK NI NI A1113 OG2 FLC A1114 1555 1555 2.23 LINK NE2 HIS B 48 NI NI B1113 1555 1555 2.19 LINK NE2 HIS B 50 NI NI B1113 1555 1555 2.08 LINK OE1 GLN B 55 NI NI B1113 1555 1555 2.19 LINK NE2 HIS B 89 NI NI B1113 1555 1555 2.10 LINK NI NI B1113 CGC FLC B1114 1555 1555 2.43 LINK NI NI B1113 OG1 FLC B1114 1555 1555 2.02 LINK NI NI B1113 OG2 FLC B1114 1555 1555 2.30 LINK NE2 HIS C 48 NI NI C1114 1555 1555 2.26 LINK NE2 HIS C 50 NI NI C1114 1555 1555 2.08 LINK OE1 GLN C 55 NI NI C1114 1555 1555 2.13 LINK NE2 HIS C 89 NI NI C1114 1555 1555 2.15 LINK NI NI C1114 OG2 FLC C1115 1555 1555 2.15 LINK NI NI C1114 OG1 FLC C1115 1555 1555 2.12 LINK NI NI C1114 CGC FLC C1115 1555 1555 2.39 LINK NE2 HIS D 48 NI NI D1113 1555 1555 2.25 LINK NE2 HIS D 50 NI NI D1113 1555 1555 2.13 LINK OE1 GLN D 55 NI NI D1113 1555 1555 2.18 LINK NE2 HIS D 89 NI NI D1113 1555 1555 2.17 LINK NI NI D1113 OG2 FLC D1114 1555 1555 2.42 LINK NI NI D1113 OG1 FLC D1114 1555 1555 2.01 LINK NI NI D1113 CGC FLC D1114 1555 1555 2.45 LINK ND1 HIS H 1 NI NI H1004 1555 1555 1.91 LINK ND1 HIS H 2 NI NI H1004 1555 1555 2.05 CISPEP 1 SER A 105 PRO A 106 0 -4.55 CISPEP 2 SER B 105 PRO B 106 0 -4.83 CISPEP 3 SER C 105 PRO C 106 0 -3.26 CISPEP 4 SER D 105 PRO D 106 0 -7.57 SITE 1 AC1 5 HIS B 48 HIS B 50 GLN B 55 HIS B 89 SITE 2 AC1 5 FLC B1114 SITE 1 AC2 5 HIS D 48 HIS D 50 GLN D 55 HIS D 89 SITE 2 AC2 5 FLC D1114 SITE 1 AC3 5 HIS A 48 HIS A 50 GLN A 55 HIS A 89 SITE 2 AC3 5 FLC A1114 SITE 1 AC4 5 HIS C 48 HIS C 50 GLN C 55 HIS C 89 SITE 2 AC4 5 FLC C1115 SITE 1 AC5 9 VAL A 17 ARG A 23 HIS A 48 HIS A 50 SITE 2 AC5 9 GLN A 55 HIS A 89 ARG A 108 MET A 111 SITE 3 AC5 9 NI A1113 SITE 1 AC6 9 ARG B 23 HIS B 48 HIS B 50 GLN B 55 SITE 2 AC6 9 HIS B 89 ARG B 108 MET B 111 NI B1113 SITE 3 AC6 9 HOH B2077 SITE 1 AC7 10 ARG C 23 HIS C 48 HIS C 50 GLN C 55 SITE 2 AC7 10 HIS C 89 ARG C 108 MET C 111 NI C1114 SITE 3 AC7 10 HOH C2020 HOH C2073 SITE 1 AC8 10 ARG D 23 HIS D 48 HIS D 50 GLN D 55 SITE 2 AC8 10 HIS D 89 ARG D 108 MET D 111 NI D1113 SITE 3 AC8 10 HOH D2041 HOH D2045 SITE 1 AC9 4 GLU C 69 HIS H 1 HIS H 2 HIS H 3 CRYST1 110.934 78.680 68.002 90.00 113.91 90.00 C 1 2 1 12 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 0.009014 0.000000 0.003997 0.00000 SCALE2 0.000000 0.012710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016086 0.00000