HEADER HYDROLASE 03-DEC-15 5FPX TITLE THE STRUCTURE OF KDGF FROM YERSINIA ENTEROCOLITICA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PECTIN DEGRADATION PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: KDGF; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEPTIDE; COMPND 8 CHAIN: E, F; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA; SOURCE 3 ORGANISM_TAXID: 393305; SOURCE 4 STRAIN: SUBSP. ENTEROCOLITICA 8081; SOURCE 5 ATCC: 9610D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A-YEKDGF; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: YERSINIA ENTEROCOLITICA; SOURCE 13 ORGANISM_TAXID: 393305; SOURCE 14 STRAIN: SUBSP. ENTEROCOLITICA 8081; SOURCE 15 ATCC: 9610D; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET28A-YEKDGF KEYWDS HYDROLASE, 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 5FPX 1 REMARK LINK REVDAT 3 15-JUN-16 5FPX 1 JRNL REVDAT 2 01-JUN-16 5FPX 1 JRNL REVDAT 1 04-MAY-16 5FPX 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 37178 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1962 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2224 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.2510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1788 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.44000 REMARK 3 B22 (A**2) : -0.84000 REMARK 3 B33 (A**2) : -1.60000 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): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.596 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1836 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1714 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2472 ; 1.827 ; 1.908 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3950 ; 0.863 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 8.299 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;32.601 ;24.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 318 ;12.593 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;24.339 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 262 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2086 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 436 ; 0.001 ; 0.020 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): 912 ; 2.112 ; 2.043 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 911 ; 2.108 ; 2.034 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1134 ; 3.345 ; 3.031 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 924 ; 2.665 ; 2.422 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): 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 : 1.20 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 THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 5FPX 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_1290065701. 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) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979490 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39140 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 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 2PFW REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.84000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.88000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.84000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.88000 REMARK 290 SMTRY3 4 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 -2 REMARK 465 LYS A 105 REMARK 465 ARG A 106 REMARK 465 ASP A 107 REMARK 465 ASP A 108 REMARK 465 PHE A 109 REMARK 465 LEU A 110 REMARK 465 LYS B 105 REMARK 465 ARG B 106 REMARK 465 ASP B 107 REMARK 465 ASP B 108 REMARK 465 PHE B 109 REMARK 465 LEU B 110 REMARK 465 HIS E 8 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 HIS B -2 CG ND1 CD2 CE1 NE2 REMARK 470 HIS F 8 CG ND1 CD2 CE1 NE2 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 71 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 71 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 PRO B 104 C - N - CA ANGL. DEV. = 11.2 DEGREES REMARK 500 PRO B 104 C - N - CD ANGL. DEV. = -31.4 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 ASN B 103 56.07 -93.94 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 ASN B 103 PRO B 104 124.12 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 A2072 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH B2035 DISTANCE = 6.01 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 NI A1105 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 46 NE2 REMARK 620 2 HIS A 48 NE2 93.2 REMARK 620 3 GLN A 53 OE1 173.6 93.2 REMARK 620 4 HIS A 87 NE2 89.2 98.2 89.4 REMARK 620 5 GLY E 1 O 88.3 171.0 85.4 90.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1105 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 46 NE2 REMARK 620 2 HIS B 48 NE2 97.4 REMARK 620 3 GLN B 53 OE1 176.2 86.4 REMARK 620 4 HIS B 87 NE2 88.7 99.9 90.5 REMARK 620 5 GLY F 1 O 87.3 167.1 89.0 92.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1105 REMARK 900 REMARK 900 RELATED ENTRIES 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. REMARK 900 RELATED ID: 5FQ0 RELATED DB: PDB REMARK 900 THE STRUCTURE OF KDGF FROM HALOMONAS SP. DBREF 5FPX A 2 110 UNP A1JMF7 A1JMF7_YERE8 2 110 DBREF 5FPX B 2 110 UNP A1JMF7 A1JMF7_YERE8 2 110 DBREF 5FPX E 1 8 PDB 5FPX 5FPX 1 8 DBREF 5FPX F 1 8 PDB 5FPX 5FPX 1 8 SEQADV 5FPX HIS A -2 UNP A1JMF7 EXPRESSION TAG SEQADV 5FPX MET A -1 UNP A1JMF7 EXPRESSION TAG SEQADV 5FPX ALA A 0 UNP A1JMF7 EXPRESSION TAG SEQADV 5FPX SER A 1 UNP A1JMF7 EXPRESSION TAG SEQADV 5FPX HIS B -2 UNP A1JMF7 EXPRESSION TAG SEQADV 5FPX MET B -1 UNP A1JMF7 EXPRESSION TAG SEQADV 5FPX ALA B 0 UNP A1JMF7 EXPRESSION TAG SEQADV 5FPX SER B 1 UNP A1JMF7 EXPRESSION TAG SEQRES 1 A 113 HIS MET ALA SER LYS MET PHE PHE ILE ASN ASP GLU THR SEQRES 2 A 113 PRO TRP GLU GLU LEU GLY ASN GLY ILE LYS ARG LYS VAL SEQRES 3 A 113 MET THR TRP SER ASP ASP LEU MET MET VAL CYS VAL HIS SEQRES 4 A 113 PHE ASP LYS GLY ALA ILE GLY VAL ALA HIS LYS HIS ASP SEQRES 5 A 113 ILE HIS ASP GLN ILE ALA TYR VAL ALA ALA GLY SER PHE SEQRES 6 A 113 GLU VAL GLU ILE GLU GLY GLN LYS ARG ILE LEU LYS ALA SEQRES 7 A 113 GLY ASP ALA TYR ARG ALA VAL LYS ASN GLU MET HIS GLY SEQRES 8 A 113 ALA VAL SER LEU GLU ASP ASN SER ILE LEU ILE ASP THR SEQRES 9 A 113 PHE ASN PRO LYS ARG ASP ASP PHE LEU SEQRES 1 B 113 HIS MET ALA SER LYS MET PHE PHE ILE ASN ASP GLU THR SEQRES 2 B 113 PRO TRP GLU GLU LEU GLY ASN GLY ILE LYS ARG LYS VAL SEQRES 3 B 113 MET THR TRP SER ASP ASP LEU MET MET VAL CYS VAL HIS SEQRES 4 B 113 PHE ASP LYS GLY ALA ILE GLY VAL ALA HIS LYS HIS ASP SEQRES 5 B 113 ILE HIS ASP GLN ILE ALA TYR VAL ALA ALA GLY SER PHE SEQRES 6 B 113 GLU VAL GLU ILE GLU GLY GLN LYS ARG ILE LEU LYS ALA SEQRES 7 B 113 GLY ASP ALA TYR ARG ALA VAL LYS ASN GLU MET HIS GLY SEQRES 8 B 113 ALA VAL SER LEU GLU ASP ASN SER ILE LEU ILE ASP THR SEQRES 9 B 113 PHE ASN PRO LYS ARG ASP ASP PHE LEU SEQRES 1 E 8 GLY SER SER HIS HIS HIS HIS HIS SEQRES 1 F 8 GLY SER SER HIS HIS HIS HIS HIS HET NI A1105 1 HET NI B1105 1 HETNAM NI NICKEL (II) ION FORMUL 5 NI 2(NI 2+) FORMUL 7 HOH *260(H2 O) HELIX 1 1 ILE A 6 THR A 10 5 5 HELIX 2 2 ILE B 6 THR B 10 5 5 SHEET 1 AA 7 PHE A 4 PHE A 5 0 SHEET 2 AA 7 ALA B 78 ALA B 81 -1 O ALA B 78 N PHE A 5 SHEET 3 AA 7 GLN B 53 ALA B 59 -1 O GLN B 53 N ALA B 81 SHEET 4 AA 7 SER B 96 PHE B 102 -1 O ILE B 97 N ALA B 58 SHEET 5 AA 7 MET B 31 PHE B 37 -1 O MET B 31 N PHE B 102 SHEET 6 AA 7 ILE B 19 TRP B 26 -1 O LYS B 20 N HIS B 36 SHEET 7 AA 7 GLU B 13 GLY B 16 -1 O GLU B 13 N ARG B 21 SHEET 1 AB 7 GLU A 13 GLY A 16 0 SHEET 2 AB 7 ILE A 19 TRP A 26 -1 O ILE A 19 N LEU A 15 SHEET 3 AB 7 MET A 31 PHE A 37 -1 O MET A 32 N MET A 24 SHEET 4 AB 7 SER A 96 PHE A 102 -1 O SER A 96 N PHE A 37 SHEET 5 AB 7 GLN A 53 ALA A 59 -1 O ILE A 54 N THR A 101 SHEET 6 AB 7 ALA A 78 ALA A 81 -1 O TYR A 79 N ALA A 55 SHEET 7 AB 7 PHE B 4 PHE B 5 -1 O PHE B 5 N ALA A 78 SHEET 1 AC 4 ILE A 42 HIS A 46 0 SHEET 2 AC 4 HIS A 87 SER A 91 -1 O HIS A 87 N HIS A 46 SHEET 3 AC 4 SER A 61 ILE A 66 -1 O GLU A 63 N VAL A 90 SHEET 4 AC 4 GLN A 69 LYS A 74 -1 O GLN A 69 N ILE A 66 SHEET 1 BA 4 ILE B 42 HIS B 46 0 SHEET 2 BA 4 HIS B 87 SER B 91 -1 O HIS B 87 N HIS B 46 SHEET 3 BA 4 SER B 61 ILE B 66 -1 O GLU B 63 N VAL B 90 SHEET 4 BA 4 GLN B 69 LYS B 74 -1 O GLN B 69 N ILE B 66 LINK NE2 HIS A 46 NI NI A1105 1555 1555 2.18 LINK NE2 HIS A 48 NI NI A1105 1555 1555 2.18 LINK OE1 GLN A 53 NI NI A1105 1555 1555 2.14 LINK NE2 HIS A 87 NI NI A1105 1555 1555 2.14 LINK NI NI A1105 O GLY E 1 1555 1555 2.10 LINK NE2 HIS B 46 NI NI B1105 1555 1555 2.17 LINK NE2 HIS B 48 NI NI B1105 1555 1555 2.11 LINK OE1 GLN B 53 NI NI B1105 1555 1555 2.16 LINK NE2 HIS B 87 NI NI B1105 1555 1555 2.15 LINK NI NI B1105 O GLY F 1 1555 1555 2.08 SITE 1 AC1 5 HIS A 46 HIS A 48 GLN A 53 HIS A 87 SITE 2 AC1 5 GLY E 1 SITE 1 AC2 5 HIS B 46 HIS B 48 GLN B 53 HIS B 87 SITE 2 AC2 5 GLY F 1 CRYST1 39.920 73.760 83.680 90.00 90.00 90.00 P 21 21 21 8 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 0.025050 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011950 0.00000