HEADER DNA BINDING PROTEIN/DNA 15-NOV-11 3VKE TITLE CONTRIBUTION OF THE FIRST K-HOMOLOGY DOMAIN OF POLY(C)-BINDING PROTEIN TITLE 2 1 TO ITS AFFINITY AND SPECIFICITY FOR C-RICH OLIGONUCLEOTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY(RC)-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: KH1 DOMAIN; COMPND 5 SYNONYM: ALPHA-CP1, HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN E1, HNRNP COMPND 6 E1, NUCLEIC ACID-BINDING PROTEIN SUB2.3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3'); COMPND 11 CHAIN: R, S, T, U; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PCBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PCBP-1, DNA RNA BINDING PROTEIN, KH DOMAIN, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.A.K.TRAORE,M.C.J.WILCE,J.A.WILCE REVDAT 3 08-NOV-23 3VKE 1 SEQADV REVDAT 2 17-JUL-13 3VKE 1 JRNL REVDAT 1 29-FEB-12 3VKE 0 JRNL AUTH Y.M.K.YOGA,D.A.K.TRAORE,M.SIDIQI,C.SZETO,N.R.PENDINI, JRNL AUTH 2 A.BARKER,P.J.LEEDMAN,J.A.WILCE,M.C.J.WILCE JRNL TITL CONTRIBUTION OF THE FIRST K-HOMOLOGY DOMAIN OF JRNL TITL 2 POLY(C)-BINDING PROTEIN 1 TO ITS AFFINITY AND SPECIFICITY JRNL TITL 3 FOR C-RICH OLIGONUCLEOTIDES JRNL REF NUCLEIC ACIDS RES. V. 40 5101 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22344691 JRNL DOI 10.1093/NAR/GKS058 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 35997 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1808 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2237 REMARK 3 NUCLEIC ACID ATOMS : 388 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.36000 REMARK 3 B22 (A**2) : 1.63000 REMARK 3 B33 (A**2) : 0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.68000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.484 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2632 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3602 ; 2.243 ; 2.159 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 293 ; 5.433 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 73 ;35.111 ;23.288 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 433 ;16.230 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;25.703 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 435 ; 0.157 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1739 ; 0.011 ; 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): 1448 ; 2.409 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2330 ; 3.962 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1184 ; 5.850 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1270 ; 8.277 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2632 ; 3.115 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3VKE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000095154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 38.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 1ZTG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PHOSPHATE-CITRATE, 40%(V/V) PEG REMARK 280 300, PH 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 57.44350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A, R 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 APPLY THE FOLLOWING TO CHAINS: B, S 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, T 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, U 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 B 12 REMARK 465 HIS C 12 REMARK 465 ILE C 83 REMARK 465 ASN C 84 REMARK 465 SER C 85 REMARK 465 SER C 86 REMARK 465 TRP C 87 REMARK 465 HIS D 12 REMARK 465 SER D 85 REMARK 465 SER D 86 REMARK 465 TRP D 87 REMARK 465 DA T 1 REMARK 465 DA T 6 REMARK 465 DA U 1 REMARK 465 DA U 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 A 34 CG CD OE1 OE2 REMARK 470 GLU B 34 CG CD OE1 OE2 REMARK 470 GLU C 34 CG CD OE1 OE2 REMARK 470 GLU C 42 CG CD OE1 OE2 REMARK 470 ASN C 66 CG OD1 ND2 REMARK 470 GLU D 34 CG CD OE1 OE2 REMARK 470 LYS D 37 CG CD CE NZ REMARK 470 ASN D 66 CG OD1 ND2 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 LYS A 23 CG CD CE NZ REMARK 480 LYS A 31 CD CE NZ REMARK 480 LYS A 32 CD CE NZ REMARK 480 ASN A 53 CG OD1 ND2 REMARK 480 GLU A 80 OE1 REMARK 480 LYS B 23 CD CE NZ REMARK 480 LYS B 31 CD CE NZ REMARK 480 GLU B 80 CD OE1 OE2 REMARK 480 LYS C 23 CG CD CE NZ REMARK 480 GLU C 24 CD OE1 OE2 REMARK 480 ARG C 38 CD NE CZ NH1 NH2 REMARK 480 ARG C 46 CD NE CZ NH1 NH2 REMARK 480 GLU C 56 CD OE1 OE2 REMARK 480 LYS C 70 CE NZ REMARK 480 ARG D 38 NE CZ NH1 NH2 REMARK 480 GLU D 42 CD OE1 OE2 REMARK 480 ARG D 46 NE CZ NH1 NH2 REMARK 480 GLU D 80 CD OE1 OE2 REMARK 480 GLU D 81 CG CD OE1 OE2 REMARK 480 DA R 1 P OP1 OP2 REMARK 480 DA S 1 P OP1 OP2 REMARK 480 DC U 2 P OP1 OP2 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 A 101 O HOH B 100 1.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OP2 DC T 2 O3' DC U 5 2656 1.41 REMARK 500 P DC T 2 O3' DC U 5 2656 1.63 REMARK 500 OP1 DC T 2 O3' DC U 5 2656 1.73 REMARK 500 O3' DC T 5 OP2 DC U 2 2556 1.75 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 LYS A 31 CG LYS A 31 CD -0.385 REMARK 500 LYS B 31 CG LYS B 31 CD -0.300 REMARK 500 ARG B 38 CZ ARG B 38 NH1 0.079 REMARK 500 LYS C 23 CB LYS C 23 CG -0.164 REMARK 500 GLU C 24 CG GLU C 24 CD 0.208 REMARK 500 GLU C 56 CG GLU C 56 CD 0.111 REMARK 500 ARG D 38 CD ARG D 38 NE 0.366 REMARK 500 GLU D 42 CG GLU D 42 CD -0.170 REMARK 500 GLU D 80 CG GLU D 80 CD -0.312 REMARK 500 DA R 1 P DA R 1 O5' -0.485 REMARK 500 DA R 6 O5' DA R 6 C5' -0.189 REMARK 500 DA R 6 N3 DA R 6 C4 0.037 REMARK 500 DA S 1 P DA S 1 O5' -0.511 REMARK 500 DA S 1 C6 DA S 1 N6 0.049 REMARK 500 DA S 6 N3 DA S 6 C4 0.038 REMARK 500 DA S 6 C5 DA S 6 N7 0.044 REMARK 500 DA S 6 N9 DA S 6 C4 0.042 REMARK 500 DC T 2 C5' DC T 2 C4' 0.066 REMARK 500 DC T 2 O4' DC T 2 C1' 0.071 REMARK 500 DC T 2 C1' DC T 2 N1 0.144 REMARK 500 DC T 2 C2 DC T 2 O2 -0.079 REMARK 500 DC T 2 N1 DC T 2 C2 0.061 REMARK 500 DC T 5 O3' DC T 5 C3' 0.097 REMARK 500 DC U 2 P DC U 2 O5' 0.314 REMARK 500 DC U 2 N1 DC U 2 C2 0.073 REMARK 500 DC U 4 N1 DC U 4 C6 0.041 REMARK 500 DC U 5 O3' DC U 5 C3' 0.108 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 LYS A 31 CB - CG - CD ANGL. DEV. = 20.3 DEGREES REMARK 500 GLU A 80 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG B 17 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 17 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 38 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG B 38 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG B 38 NE - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG C 40 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG C 40 NE - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 GLU C 56 CB - CG - CD ANGL. DEV. = -19.9 DEGREES REMARK 500 ARG D 17 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG D 40 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG D 40 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 GLU D 80 CG - CD - OE1 ANGL. DEV. = -17.9 DEGREES REMARK 500 DA R 1 P - O5' - C5' ANGL. DEV. = 28.2 DEGREES REMARK 500 DA R 1 C6 - N1 - C2 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC R 2 N1 - C2 - O2 ANGL. DEV. = 5.4 DEGREES REMARK 500 DC R 3 O4' - C1' - N1 ANGL. DEV. = -6.9 DEGREES REMARK 500 DC R 5 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 DA R 6 O5' - C5' - C4' ANGL. DEV. = -11.3 DEGREES REMARK 500 DA R 6 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DA R 6 C4' - C3' - C2' ANGL. DEV. = -10.4 DEGREES REMARK 500 DA R 6 N1 - C2 - N3 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA R 6 N1 - C6 - N6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA S 1 O5' - C5' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 DA S 1 P - O5' - C5' ANGL. DEV. = 14.6 DEGREES REMARK 500 DA S 1 C6 - N1 - C2 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA S 1 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 DC S 3 O4' - C1' - N1 ANGL. DEV. = -5.7 DEGREES REMARK 500 DC S 3 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA S 6 N9 - C1' - C2' ANGL. DEV. = 8.8 DEGREES REMARK 500 DA S 6 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA S 6 N1 - C2 - N3 ANGL. DEV. = -4.1 DEGREES REMARK 500 DA S 6 C2 - N3 - C4 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA S 6 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA S 6 C5 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC T 2 O5' - C5' - C4' ANGL. DEV. = 19.0 DEGREES REMARK 500 DC T 2 C5' - C4' - O4' ANGL. DEV. = 12.4 DEGREES REMARK 500 DC T 2 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 DC T 2 C6 - N1 - C2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DC T 2 N1 - C2 - N3 ANGL. DEV. = 8.8 DEGREES REMARK 500 DC T 2 C2 - N3 - C4 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC T 2 C4 - C5 - C6 ANGL. DEV. = 8.1 DEGREES REMARK 500 DC T 2 N1 - C2 - O2 ANGL. DEV. = 7.4 DEGREES REMARK 500 DC T 2 N3 - C2 - O2 ANGL. DEV. = -16.3 DEGREES REMARK 500 DC T 2 C2 - N1 - C1' ANGL. DEV. = 10.0 DEGREES REMARK 500 DC T 3 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC U 2 P - O5' - C5' ANGL. DEV. = -16.6 DEGREES REMARK 500 DC U 2 C6 - N1 - C2 ANGL. DEV. = -3.2 DEGREES REMARK 500 DC U 2 C2 - N3 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 ANGLE DEVIATIONS. 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 53 47.14 -91.74 REMARK 500 LYS D 32 25.10 49.90 REMARK 500 ASN D 53 59.25 -103.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 80 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZTG RELATED DB: PDB DBREF 3VKE A 14 86 UNP Q15365 PCBP1_HUMAN 14 86 DBREF 3VKE B 14 86 UNP Q15365 PCBP1_HUMAN 14 86 DBREF 3VKE C 14 86 UNP Q15365 PCBP1_HUMAN 14 86 DBREF 3VKE D 14 86 UNP Q15365 PCBP1_HUMAN 14 86 DBREF 3VKE R 1 6 PDB 3VKE 3VKE 1 6 DBREF 3VKE S 1 6 PDB 3VKE 3VKE 1 6 DBREF 3VKE T 1 6 PDB 3VKE 3VKE 1 6 DBREF 3VKE U 1 6 PDB 3VKE 3VKE 1 6 SEQADV 3VKE HIS A 12 UNP Q15365 EXPRESSION TAG SEQADV 3VKE MET A 13 UNP Q15365 EXPRESSION TAG SEQADV 3VKE SER A 54 UNP Q15365 CYS 54 ENGINEERED MUTATION SEQADV 3VKE TRP A 87 UNP Q15365 EXPRESSION TAG SEQADV 3VKE HIS B 12 UNP Q15365 EXPRESSION TAG SEQADV 3VKE MET B 13 UNP Q15365 EXPRESSION TAG SEQADV 3VKE SER B 54 UNP Q15365 CYS 54 ENGINEERED MUTATION SEQADV 3VKE TRP B 87 UNP Q15365 EXPRESSION TAG SEQADV 3VKE HIS C 12 UNP Q15365 EXPRESSION TAG SEQADV 3VKE MET C 13 UNP Q15365 EXPRESSION TAG SEQADV 3VKE SER C 54 UNP Q15365 CYS 54 ENGINEERED MUTATION SEQADV 3VKE TRP C 87 UNP Q15365 EXPRESSION TAG SEQADV 3VKE HIS D 12 UNP Q15365 EXPRESSION TAG SEQADV 3VKE MET D 13 UNP Q15365 EXPRESSION TAG SEQADV 3VKE SER D 54 UNP Q15365 CYS 54 ENGINEERED MUTATION SEQADV 3VKE TRP D 87 UNP Q15365 EXPRESSION TAG SEQRES 1 A 76 HIS MET LEU THR ILE ARG LEU LEU MET HIS GLY LYS GLU SEQRES 2 A 76 VAL GLY SER ILE ILE GLY LYS LYS GLY GLU SER VAL LYS SEQRES 3 A 76 ARG ILE ARG GLU GLU SER GLY ALA ARG ILE ASN ILE SER SEQRES 4 A 76 GLU GLY ASN SER PRO GLU ARG ILE ILE THR LEU THR GLY SEQRES 5 A 76 PRO THR ASN ALA ILE PHE LYS ALA PHE ALA MET ILE ILE SEQRES 6 A 76 ASP LYS LEU GLU GLU ASP ILE ASN SER SER TRP SEQRES 1 B 76 HIS MET LEU THR ILE ARG LEU LEU MET HIS GLY LYS GLU SEQRES 2 B 76 VAL GLY SER ILE ILE GLY LYS LYS GLY GLU SER VAL LYS SEQRES 3 B 76 ARG ILE ARG GLU GLU SER GLY ALA ARG ILE ASN ILE SER SEQRES 4 B 76 GLU GLY ASN SER PRO GLU ARG ILE ILE THR LEU THR GLY SEQRES 5 B 76 PRO THR ASN ALA ILE PHE LYS ALA PHE ALA MET ILE ILE SEQRES 6 B 76 ASP LYS LEU GLU GLU ASP ILE ASN SER SER TRP SEQRES 1 C 76 HIS MET LEU THR ILE ARG LEU LEU MET HIS GLY LYS GLU SEQRES 2 C 76 VAL GLY SER ILE ILE GLY LYS LYS GLY GLU SER VAL LYS SEQRES 3 C 76 ARG ILE ARG GLU GLU SER GLY ALA ARG ILE ASN ILE SER SEQRES 4 C 76 GLU GLY ASN SER PRO GLU ARG ILE ILE THR LEU THR GLY SEQRES 5 C 76 PRO THR ASN ALA ILE PHE LYS ALA PHE ALA MET ILE ILE SEQRES 6 C 76 ASP LYS LEU GLU GLU ASP ILE ASN SER SER TRP SEQRES 1 D 76 HIS MET LEU THR ILE ARG LEU LEU MET HIS GLY LYS GLU SEQRES 2 D 76 VAL GLY SER ILE ILE GLY LYS LYS GLY GLU SER VAL LYS SEQRES 3 D 76 ARG ILE ARG GLU GLU SER GLY ALA ARG ILE ASN ILE SER SEQRES 4 D 76 GLU GLY ASN SER PRO GLU ARG ILE ILE THR LEU THR GLY SEQRES 5 D 76 PRO THR ASN ALA ILE PHE LYS ALA PHE ALA MET ILE ILE SEQRES 6 D 76 ASP LYS LEU GLU GLU ASP ILE ASN SER SER TRP SEQRES 1 R 6 DA DC DC DC DC DA SEQRES 1 S 6 DA DC DC DC DC DA SEQRES 1 T 6 DA DC DC DC DC DA SEQRES 1 U 6 DA DC DC DC DC DA FORMUL 9 HOH *71(H2 O) HELIX 1 1 GLY A 22 GLY A 30 1 9 HELIX 2 2 GLY A 33 GLY A 44 1 12 HELIX 3 3 THR A 65 ASP A 82 1 18 HELIX 4 4 GLY B 22 GLY B 30 1 9 HELIX 5 5 GLY B 33 GLY B 44 1 12 HELIX 6 6 PRO B 64 SER B 86 1 23 HELIX 7 7 GLY C 22 GLY C 30 1 9 HELIX 8 8 GLY C 33 GLY C 44 1 12 HELIX 9 9 PRO C 64 ASP C 82 1 19 HELIX 10 10 GLY D 22 GLY D 30 1 9 HELIX 11 11 GLY D 33 GLY D 44 1 12 HELIX 12 12 PRO D 64 ILE D 83 1 20 SHEET 1 A 6 ARG A 46 ILE A 49 0 SHEET 2 A 6 GLU A 56 PRO A 64 -1 O THR A 60 N ASN A 48 SHEET 3 A 6 MET A 13 HIS A 21 -1 N ILE A 16 O LEU A 61 SHEET 4 A 6 LEU C 14 HIS C 21 -1 O LEU C 19 N ARG A 17 SHEET 5 A 6 GLU C 56 GLY C 63 -1 O ILE C 59 N LEU C 18 SHEET 6 A 6 ARG C 46 ILE C 49 -1 N ASN C 48 O THR C 60 SHEET 1 B 6 ARG B 46 ILE B 49 0 SHEET 2 B 6 GLU B 56 GLY B 63 -1 O THR B 60 N ASN B 48 SHEET 3 B 6 LEU B 14 HIS B 21 -1 N LEU B 18 O ILE B 59 SHEET 4 B 6 LEU D 14 HIS D 21 -1 O LEU D 19 N ARG B 17 SHEET 5 B 6 GLU D 56 GLY D 63 -1 O ILE D 59 N LEU D 18 SHEET 6 B 6 ARG D 46 ILE D 49 -1 N ASN D 48 O THR D 60 CISPEP 1 ILE D 83 ASN D 84 0 6.32 CRYST1 38.597 114.887 43.429 90.00 93.73 90.00 P 1 21 1 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 0.025909 0.000000 0.001689 0.00000 SCALE2 0.000000 0.008704 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023075 0.00000