HEADER HYDROLASE 13-NOV-15 5EQV TITLE 1.45 ANGSTROM CRYSTAL STRUCTURE OF BIFUNCTIONAL 2',3'-CYCLIC TITLE 2 NUCLEOTIDE 2'-PHOSPHODIESTERASE/3'-NUCLEOTIDASE PERIPLASMIC PRECURSOR TITLE 3 PROTEIN FROM YERSINIA PESTIS WITH PHOSPHATE BOUND TO THE ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL 2',3'-CYCLIC NUCLEOTIDE 2'- COMPND 3 PHOSPHODIESTERASE/3'-NUCLEOTIDASE PERIPLASMIC PRECURSOR PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 22-358; COMPND 6 EC: 3.1.4.16; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS CO92; SOURCE 3 ORGANISM_TAXID: 214092; SOURCE 4 GENE: CPDB, AK38_3205; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMCSG53 KEYWDS BIFUNCTIONAL 2', 3'-CYCLIC NUCLEOTIDE, 2'-PHOSPHODIESTERASE/3'- KEYWDS 2 NUCLEOTIDASE, PERIPLASMIC PRECURSOR PROTEIN, CSGID, STRUCTURAL KEYWDS 3 GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, KEYWDS 4 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.MINASOV,L.SHUVALOVA,J.S.BRUNZELLE,O.KIRYUKHINA,I.DUBROVSKA, AUTHOR 2 S.GRIMSHAW,K.KWON,W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF AUTHOR 3 INFECTIOUS DISEASES (CSGID) REVDAT 2 06-MAR-24 5EQV 1 REMARK LINK REVDAT 1 25-NOV-15 5EQV 0 JRNL AUTH G.MINASOV,L.SHUVALOVA,J.S.BRUNZELLE,O.KIRYUKHINA, JRNL AUTH 2 I.DUBROVSKA,S.GRIMSHAW,K.KWON,W.F.ANDERSON, JRNL AUTH 3 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES JRNL AUTH 4 (CSGID) JRNL TITL 1.45 ANGSTROM CRYSTAL STRUCTURE OF BIFUNCTIONAL 2',3'-CYCLIC JRNL TITL 2 NUCLEOTIDE 2'-PHOSPHODIESTERASE/3'-NUCLEOTIDASE PERIPLASMIC JRNL TITL 3 PRECURSOR PROTEIN FROM YERSINIA PESTIS WITH PHOSPHATE BOUND JRNL TITL 4 TO THE ACTIVE SITE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 62495 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) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3280 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4519 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE SET COUNT : 237 REMARK 3 BIN FREE R VALUE : 0.1910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2592 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 629 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : 2.13000 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.679 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2881 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2738 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3942 ; 1.477 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6335 ; 0.913 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 379 ; 5.205 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;39.575 ;25.591 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 483 ;10.691 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.022 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3403 ; 0.023 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 640 ; 0.019 ; 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): 1454 ; 0.946 ; 1.320 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1452 ; 0.939 ; 1.317 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1853 ; 1.475 ; 1.977 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1854 ; 1.477 ; 1.978 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1427 ; 1.562 ; 1.557 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1427 ; 1.556 ; 1.557 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2090 ; 2.449 ; 2.242 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3926 ; 7.111 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3414 ; 6.229 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4 ; 4.585 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7 ; 9.502 ; 5.000 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 27 A 104 REMARK 3 ORIGIN FOR THE GROUP (A): -4.7478 25.2939 9.4529 REMARK 3 T TENSOR REMARK 3 T11: 0.0292 T22: 0.0211 REMARK 3 T33: 0.0080 T12: -0.0040 REMARK 3 T13: 0.0053 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.8115 L22: 0.6823 REMARK 3 L33: 0.9751 L12: 0.1856 REMARK 3 L13: -0.0845 L23: -0.1655 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: 0.0843 S13: 0.0703 REMARK 3 S21: -0.0796 S22: 0.0346 S23: 0.0111 REMARK 3 S31: -0.0148 S32: -0.0302 S33: -0.0249 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 105 A 312 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3972 28.8106 21.2848 REMARK 3 T TENSOR REMARK 3 T11: 0.0179 T22: 0.0230 REMARK 3 T33: 0.0110 T12: 0.0033 REMARK 3 T13: 0.0014 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 0.6498 L22: 0.6214 REMARK 3 L33: 0.3516 L12: 0.2891 REMARK 3 L13: -0.0886 L23: -0.0835 REMARK 3 S TENSOR REMARK 3 S11: 0.0042 S12: -0.0278 S13: -0.0225 REMARK 3 S21: 0.0211 S22: -0.0191 S23: -0.0753 REMARK 3 S31: -0.0048 S32: 0.0243 S33: 0.0149 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 313 A 362 REMARK 3 ORIGIN FOR THE GROUP (A): -5.7661 20.2063 10.5898 REMARK 3 T TENSOR REMARK 3 T11: 0.0557 T22: 0.0548 REMARK 3 T33: 0.0357 T12: -0.0060 REMARK 3 T13: 0.0053 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.9950 L22: 0.7729 REMARK 3 L33: 0.4995 L12: 0.0813 REMARK 3 L13: 0.0216 L23: 0.2822 REMARK 3 S TENSOR REMARK 3 S11: 0.0130 S12: 0.1060 S13: -0.0061 REMARK 3 S21: -0.1052 S22: 0.0080 S23: 0.0202 REMARK 3 S31: 0.0679 S32: 0.0143 S33: -0.0210 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 REMARK 4 REMARK 4 5EQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215378. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : C(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65853 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 42.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 0.54500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.300 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: PDB3JYF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 8.6 MG/ML, 0.01M TRIS-HCL (PH REMARK 280 8.3), 5MM THYMIDINE; SCREEN: CLASSICS II (F11), 0.2M SODIUM REMARK 280 CHLORIDE, 0.1M BIS-TRIS (PH 6.5), 25% (W/V) PEG 3350;, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 31.67850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.64100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.64100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 47.51775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.64100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.64100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.83925 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.64100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.64100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 47.51775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.64100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.64100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 15.83925 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 31.67850 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: 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 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 760 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 SER A 23 REMARK 465 ASN A 24 REMARK 465 ALA A 25 REMARK 465 SER A 26 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 62 NE - CZ - NH1 ANGL. DEV. = 3.0 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 LYS A 142 40.32 -89.90 REMARK 500 MET A 244 6.78 80.64 REMARK 500 HIS A 265 -43.01 75.33 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 A1124 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A1125 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A1126 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A1127 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1128 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A1129 DISTANCE = 6.44 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 FE A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 39 OD1 REMARK 620 2 HIS A 41 NE2 101.5 REMARK 620 3 ASP A 84 OD2 85.9 94.3 REMARK 620 4 HIS A 267 NE2 87.2 95.8 168.7 REMARK 620 5 PO4 A 405 O2 168.1 89.1 88.0 97.1 REMARK 620 6 HOH A 616 O 80.3 171.4 77.4 92.6 88.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 77 O REMARK 620 2 SER A 77 O 8.8 REMARK 620 3 HOH A 625 O 72.4 65.1 REMARK 620 4 HOH A 852 O 79.3 84.5 89.2 REMARK 620 5 HOH A 878 O 84.6 80.0 89.7 163.5 REMARK 620 6 HOH A 878 O 87.5 86.1 111.8 150.6 22.6 REMARK 620 7 HOH A 900 O 102.4 110.5 169.0 80.2 99.6 77.1 REMARK 620 8 HOH A 997 O 166.1 157.7 94.0 103.7 92.8 95.4 91.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 84 OD2 REMARK 620 2 ASN A 124 OD1 101.5 REMARK 620 3 HIS A 233 NE2 85.7 83.4 REMARK 620 4 HIS A 265 ND1 167.4 90.0 90.6 REMARK 620 5 PO4 A 405 O4 89.5 90.7 171.5 95.6 REMARK 620 6 HOH A 616 O 76.6 176.7 99.0 92.2 86.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 617 O REMARK 620 2 HOH A 802 O 81.6 REMARK 620 3 HOH A 893 O 84.3 165.8 REMARK 620 4 HOH A 955 O 93.9 92.5 87.7 REMARK 620 5 HOH A1031 O 161.9 85.2 108.8 99.0 REMARK 620 6 HOH A1114 O 79.6 96.1 82.0 168.3 89.7 REMARK 620 7 HOH A1114 O 86.7 109.3 70.5 158.1 86.1 14.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MLT A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CSGID-IDP02613 RELATED DB: TARGETTRACK DBREF1 5EQV A 26 362 UNP A0A0B6NVJ4_YERPE DBREF2 5EQV A A0A0B6NVJ4 22 358 SEQADV 5EQV SER A 23 UNP A0A0B6NVJ EXPRESSION TAG SEQADV 5EQV ASN A 24 UNP A0A0B6NVJ EXPRESSION TAG SEQADV 5EQV ALA A 25 UNP A0A0B6NVJ EXPRESSION TAG SEQRES 1 A 340 SER ASN ALA SER ALA ALA THR VAL ASP LEU ARG VAL LEU SEQRES 2 A 340 GLU THR THR ASP LEU HIS SER ASN MET MET ASP PHE ASP SEQRES 3 A 340 TYR TYR LYS ASP LYS PRO THR GLU LYS PHE GLY LEU VAL SEQRES 4 A 340 ARG THR ALA SER LEU ILE ILE ALA ALA ARG GLN GLN ALA SEQRES 5 A 340 THR ASN SER VAL LEU VAL ASP ASN GLY ASP VAL ILE GLN SEQRES 6 A 340 GLY SER PRO LEU GLY ASP TYR ILE ALA ALA LYS GLY LEU SEQRES 7 A 340 ASN ASP GLY GLU ILE HIS PRO VAL TYR LYS ALA MET ASN SEQRES 8 A 340 THR LEU ASP TYR ALA VAL GLY ASN ILE GLY ASN HIS GLU SEQRES 9 A 340 PHE ASN TYR GLY LEU ASP TYR LEU LYS LYS SER LEU ALA SEQRES 10 A 340 GLY ALA LYS PHE PRO TYR VAL ASN ALA ASN VAL ILE ASP SEQRES 11 A 340 VAL LYS THR GLY LYS PRO LEU PHE GLN PRO TYR LEU ILE SEQRES 12 A 340 ILE ASP THR PRO VAL LYS ASP ARG ASP GLY LYS SER HIS SEQRES 13 A 340 ASN LEU ARG ILE GLY TYR ILE GLY PHE VAL PRO PRO GLN SEQRES 14 A 340 VAL MET ILE TRP ASP LYS ALA ASN LEU SER GLY LYS VAL SEQRES 15 A 340 THR VAL ASN ASP ILE THR GLU THR ALA LYS LYS TRP VAL SEQRES 16 A 340 PRO GLU MET ARG GLU GLN GLY ALA ASP LEU VAL VAL ALA SEQRES 17 A 340 ILE PRO HIS SER GLY LEU SER SER ASP PRO TYR LYS THR SEQRES 18 A 340 MET ALA GLU ASN SER VAL TYR TYR LEU SER GLN VAL PRO SEQRES 19 A 340 GLY ILE ASP ALA ILE MET PHE GLY HIS ALA HIS GLY VAL SEQRES 20 A 340 PHE PRO SER LYS ASP PHE ALA ALA ILE LYS GLY ALA ASP SEQRES 21 A 340 ILE THR GLN GLY THR LEU ASN GLY ILE PRO ALA VAL MET SEQRES 22 A 340 PRO GLY GLN TRP GLY ASP HIS LEU GLY VAL VAL ASP PHE SEQRES 23 A 340 VAL LEU ASN ASN ASP GLN GLY LYS TRP GLN VAL ILE ASP SEQRES 24 A 340 ALA LYS ALA GLU ALA ARG PRO ILE TYR ASP LYS THR ALA SEQRES 25 A 340 GLN LYS SER LEU ALA ALA GLU ASN ALA LYS LEU VAL GLU SEQRES 26 A 340 VAL LEU ALA VAL ASP HIS GLN SER THR ARG ASP PHE VAL SEQRES 27 A 340 SER GLN HET FE A 401 1 HET FE A 402 1 HET NA A 403 1 HET NA A 404 1 HET PO4 A 405 5 HET MLT A 406 9 HET PGE A 407 10 HET TRS A 408 8 HETNAM FE FE (III) ION HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM MLT D-MALATE HETNAM PGE TRIETHYLENE GLYCOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN MLT (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID HETSYN TRS TRIS BUFFER FORMUL 2 FE 2(FE 3+) FORMUL 4 NA 2(NA 1+) FORMUL 6 PO4 O4 P 3- FORMUL 7 MLT C4 H6 O5 FORMUL 8 PGE C6 H14 O4 FORMUL 9 TRS C4 H12 N O3 1+ FORMUL 10 HOH *629(H2 O) HELIX 1 AA1 GLY A 59 ALA A 74 1 16 HELIX 2 AA2 SER A 89 GLY A 99 1 11 HELIX 3 AA3 HIS A 106 ASN A 113 1 8 HELIX 4 AA4 GLY A 123 ASN A 128 5 6 HELIX 5 AA5 GLY A 130 GLY A 140 1 11 HELIX 6 AA6 GLN A 191 ASP A 196 1 6 HELIX 7 AA7 ASP A 196 SER A 201 1 6 HELIX 8 AA8 ASP A 208 GLN A 223 1 16 HELIX 9 AA9 SER A 248 SER A 253 1 6 HELIX 10 AB1 SER A 272 ALA A 276 5 5 HELIX 11 AB2 ASN A 342 GLN A 362 1 21 SHEET 1 AA1 6 TYR A 145 VAL A 146 0 SHEET 2 AA1 6 VAL A 119 ASN A 121 1 N GLY A 120 O VAL A 146 SHEET 3 AA1 6 SER A 77 ASP A 81 1 N ASP A 81 O ASN A 121 SHEET 4 AA1 6 THR A 29 THR A 37 1 N LEU A 35 O VAL A 78 SHEET 5 AA1 6 HIS A 302 ASN A 311 -1 O PHE A 308 N LEU A 32 SHEET 6 AA1 6 GLN A 318 PRO A 328 -1 O LYS A 323 N ASP A 307 SHEET 1 AA2 2 PHE A 47 ASP A 48 0 SHEET 2 AA2 2 LYS A 53 PRO A 54 -1 O LYS A 53 N ASP A 48 SHEET 1 AA3 2 VAL A 150 ASP A 152 0 SHEET 2 AA3 2 VAL A 204 VAL A 206 -1 O THR A 205 N ILE A 151 SHEET 1 AA4 6 TYR A 163 LYS A 171 0 SHEET 2 AA4 6 SER A 177 PHE A 187 -1 O ILE A 182 N ILE A 166 SHEET 3 AA4 6 LEU A 227 PRO A 232 1 O VAL A 229 N GLY A 183 SHEET 4 AA4 6 ALA A 260 MET A 262 1 O MET A 262 N ALA A 230 SHEET 5 AA4 6 ILE A 291 PRO A 296 1 O PRO A 292 N ILE A 261 SHEET 6 AA4 6 VAL A 269 PHE A 270 -1 N PHE A 270 O MET A 295 SHEET 1 AA5 7 TYR A 163 LYS A 171 0 SHEET 2 AA5 7 SER A 177 PHE A 187 -1 O ILE A 182 N ILE A 166 SHEET 3 AA5 7 LEU A 227 PRO A 232 1 O VAL A 229 N GLY A 183 SHEET 4 AA5 7 ALA A 260 MET A 262 1 O MET A 262 N ALA A 230 SHEET 5 AA5 7 ILE A 291 PRO A 296 1 O PRO A 292 N ILE A 261 SHEET 6 AA5 7 THR A 287 LEU A 288 -1 N LEU A 288 O ILE A 291 SHEET 7 AA5 7 ALA A 281 ASP A 282 -1 N ASP A 282 O THR A 287 SHEET 1 AA6 2 TYR A 330 ASP A 331 0 SHEET 2 AA6 2 LYS A 336 SER A 337 -1 O LYS A 336 N ASP A 331 LINK OD1 ASP A 39 FE FE A 402 1555 1555 2.18 LINK NE2 HIS A 41 FE FE A 402 1555 1555 2.20 LINK O ASER A 77 NA NA A 404 1555 1555 2.44 LINK O BSER A 77 NA NA A 404 1555 1555 2.60 LINK OD2 ASP A 84 FE FE A 401 1555 1555 2.31 LINK OD2 ASP A 84 FE FE A 402 1555 1555 2.28 LINK OD1 ASN A 124 FE FE A 401 1555 1555 2.16 LINK NE2 HIS A 233 FE FE A 401 1555 1555 2.21 LINK ND1 HIS A 265 FE FE A 401 1555 1555 2.28 LINK NE2 HIS A 267 FE FE A 402 1555 1555 2.19 LINK FE FE A 401 O4 PO4 A 405 1555 1555 2.04 LINK FE FE A 401 O HOH A 616 1555 1555 2.10 LINK FE FE A 402 O2 PO4 A 405 1555 1555 2.15 LINK FE FE A 402 O HOH A 616 1555 1555 2.08 LINK NA NA A 403 O HOH A 617 1555 1555 2.30 LINK NA NA A 403 O HOH A 802 1555 1555 2.31 LINK NA NA A 403 O HOH A 893 1555 1555 2.39 LINK NA NA A 403 O HOH A 955 1555 1555 2.37 LINK NA NA A 403 O HOH A1031 1555 1555 2.52 LINK NA NA A 403 O HOH A1114 1555 1555 2.61 LINK NA NA A 403 O HOH A1114 1555 7556 2.49 LINK NA NA A 404 O HOH A 625 1555 1555 2.50 LINK NA NA A 404 O AHOH A 852 1555 1555 2.44 LINK NA NA A 404 O AHOH A 878 1555 1555 2.47 LINK NA NA A 404 O BHOH A 878 1555 1555 2.64 LINK NA NA A 404 O HOH A 900 1555 1555 2.18 LINK NA NA A 404 O HOH A 997 1555 1555 2.29 CISPEP 1 PHE A 270 PRO A 271 0 0.08 SITE 1 AC1 7 ASP A 84 ASN A 124 HIS A 233 HIS A 265 SITE 2 AC1 7 FE A 402 PO4 A 405 HOH A 616 SITE 1 AC2 7 ASP A 39 HIS A 41 ASP A 84 HIS A 267 SITE 2 AC2 7 FE A 401 PO4 A 405 HOH A 616 SITE 1 AC3 6 HOH A 617 HOH A 802 HOH A 893 HOH A 955 SITE 2 AC3 6 HOH A1031 HOH A1114 SITE 1 AC4 6 SER A 77 HOH A 625 HOH A 852 HOH A 878 SITE 2 AC4 6 HOH A 900 HOH A 997 SITE 1 AC5 14 HIS A 41 ASP A 84 ASN A 124 HIS A 125 SITE 2 AC5 14 HIS A 265 HIS A 267 FE A 401 FE A 402 SITE 3 AC5 14 MLT A 406 HOH A 502 HOH A 524 HOH A 543 SITE 4 AC5 14 HOH A 616 HOH A 643 SITE 1 AC6 8 ASN A 124 HIS A 125 TRP A 195 GLU A 246 SITE 2 AC6 8 PO4 A 405 HOH A 502 HOH A 662 HOH A 731 SITE 1 AC7 5 THR A 210 LYS A 214 TYR A 241 HOH A 590 SITE 2 AC7 5 HOH A 760 SITE 1 AC8 9 ASN A 43 ASP A 48 TYR A 50 PHE A 58 SITE 2 AC8 9 SER A 89 HOH A 538 HOH A 545 HOH A 634 SITE 3 AC8 9 HOH A 860 CRYST1 107.282 107.282 63.357 90.00 90.00 90.00 P 43 21 2 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 0.009321 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015784 0.00000