HEADER FLUORESCENT PROTEIN/PROTEIN BINDING 06-SEP-11 3VHT TITLE CRYSTAL STRUCTURE OF GFP-WRNIP1 UBZ DOMAIN FUSION PROTEIN IN COMPLEX TITLE 2 WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GREEN FLUORESCENT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GFP DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GREEN FLUORESCENT PROTEIN,ATPASE WRNIP1; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: GFP,WRNIP1 UBZ DOMAIN (UNP RESIDUES 9-46); COMPND 10 SYNONYM: WERNER HELICASE-INTERACTING PROTEIN 1; COMPND 11 EC: 3.6.1.3; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: THE FUSION PROTEIN OF YEAST ENHANCED GREEN FLUORESCENT COMPND 14 PROTEIN, LINKER (GLY-SER) AND HUMAN WRNIP1 UBZ; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: UBIQUITIN; COMPND 17 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA; SOURCE 3 ORGANISM_COMMON: JELLYFISH; SOURCE 4 ORGANISM_TAXID: 6100; SOURCE 5 GENE: GFP; 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: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: AEQUOREA VICTORIA, HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: JELLYFISH, HUMAN; SOURCE 14 ORGANISM_TAXID: 6100, 9606; SOURCE 15 GENE: GFP, WRNIP1, WHIP; 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: PET28; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 23 ORGANISM_COMMON: MOUSE; SOURCE 24 ORGANISM_TAXID: 10090 KEYWDS GREEN FLUORESCENT PROTEIN, FUSION PROTEIN, ZINC FINGER, UBIQUITIN- KEYWDS 2 BINDING DOMAIN, FLUORESCENT PROTEIN-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.SUZUKI,S.WAKATSUKI,M.KAWASAKI REVDAT 5 06-DEC-23 3VHT 1 REMARK REVDAT 4 08-NOV-23 3VHT 1 REMARK LINK REVDAT 3 28-JUN-17 3VHT 1 COMPND SOURCE DBREF REVDAT 2 01-JUN-16 3VHT 1 JRNL REVDAT 1 10-OCT-12 3VHT 0 JRNL AUTH N.SUZUKI,A.ROHAIM,R.KATO,I.DIKIC,S.WAKATSUKI,M.KAWASAKI JRNL TITL A NOVEL MODE OF UBIQUITIN RECOGNITION BY THE JRNL TITL 2 UBIQUITIN-BINDING ZINC FINGER DOMAIN OF WRNIP1. JRNL REF FEBS J. 2016 JRNL REFN ISSN 1742-464X JRNL PMID 27062441 JRNL DOI 10.1111/FEBS.13734 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 25484 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1809 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4497 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.13000 REMARK 3 B22 (A**2) : -1.24000 REMARK 3 B33 (A**2) : 0.11000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.248 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.892 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4597 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6202 ; 1.820 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 557 ; 7.134 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 221 ;36.195 ;25.204 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 804 ;18.834 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.778 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 677 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7737 ; 0.005 ; 0.020 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): 2792 ; 0.912 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4507 ; 1.785 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1805 ; 2.901 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1695 ; 4.722 ; 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): 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 231 REMARK 3 RESIDUE RANGE : B 2 B 229 REMARK 3 RESIDUE RANGE : B 237 B 270 REMARK 3 RESIDUE RANGE : C 1 C 76 REMARK 3 ORIGIN FOR THE GROUP (A): -14.8285 -56.4302 -10.6721 REMARK 3 T TENSOR REMARK 3 T11: 0.0483 T22: 0.0450 REMARK 3 T33: 0.0328 T12: 0.0127 REMARK 3 T13: -0.0297 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 0.6759 L22: 1.0357 REMARK 3 L33: 0.9658 L12: 0.2402 REMARK 3 L13: -0.0375 L23: 0.5445 REMARK 3 S TENSOR REMARK 3 S11: -0.0052 S12: 0.0982 S13: 0.0860 REMARK 3 S21: -0.0756 S22: -0.0649 S23: 0.0931 REMARK 3 S31: -0.0623 S32: 0.0438 S33: 0.0701 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: NULL REMARK 4 REMARK 4 3VHT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000095061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 75.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3AI5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M DL-MALIC ACID, 20% PEG 3350, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 53.43200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.43200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.47500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.84600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.47500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.84600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 53.43200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.47500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.84600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 53.43200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.47500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.84600 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 SER A 232 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 THR B 230 REMARK 465 GLY B 231 REMARK 465 SER B 232 REMARK 465 ASP B 233 REMARK 465 PRO B 234 REMARK 465 PHE B 235 REMARK 465 LEU B 236 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 OE1 GLU A 111 O HOH A 550 2.17 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 TYR B 106 CD1 TYR B 106 CE1 0.101 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 B 215 NE - CZ - NH2 ANGL. DEV. = -3.1 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 A 23 47.36 36.74 REMARK 500 GLU A 172 -38.37 -32.10 REMARK 500 ASP B 103 -163.93 -163.84 REMARK 500 TYR B 143 74.29 -101.27 REMARK 500 ASN B 212 30.17 -96.71 REMARK 500 GLN B 248 -2.88 74.37 REMARK 500 THR C 9 31.07 -91.67 REMARK 500 ALA C 46 59.25 31.32 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 ARG B 96 THR B 97 149.64 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 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 244 SG REMARK 620 2 CYS B 247 SG 109.9 REMARK 620 3 HIS B 259 NE2 100.4 113.5 REMARK 620 4 CYS B 263 SG 120.0 105.0 108.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VHS RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 (1) THE SEQUENCE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN NOT REMARK 999 CURRENTLY EXIST IN UNIPROT. THIS SEQUENCE IS FOUND IN GENBANK WITH REMARK 999 ACCESSION CODE: ABI82055. (2) IN THE CHAIN A, RESIDUES -2, -1, 0, REMARK 999 231, 232 ARE EXPRESSION TAGS. (3) THE CHAIN B IS FUSION PROTEIN OF REMARK 999 YEAST ENHANCED GREEN FLUORESCENT PROTEIN (RESIDUES 1-230), LINKER REMARK 999 (GLY-SER) AND HUMAN WRNIP1 (RESIDUES 9-46). RESIDUES -2, -1, 0 ARE REMARK 999 EXPRESSION TAGS. DBREF 3VHT A -2 232 PDB 3VHT 3VHT -2 232 DBREF 3VHT B -2 230 PDB 3VHT 3VHT -2 230 DBREF 3VHT B 233 270 UNP Q96S55 WRIP1_HUMAN 9 46 DBREF 3VHT C 1 76 UNP P62983 RS27A_MOUSE 1 76 SEQADV 3VHT GLY B 231 UNP Q96S55 LINKER SEQADV 3VHT SER B 232 UNP Q96S55 LINKER SEQRES 1 A 233 GLY SER HIS MET SER LYS GLY GLU GLU LEU PHE THR GLY SEQRES 2 A 233 VAL VAL PRO ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN SEQRES 3 A 233 GLY HIS LYS PHE SER VAL SER GLY GLU GLY GLU GLY ASP SEQRES 4 A 233 ALA THR TYR GLY LYS LEU THR LEU LYS PHE ILE CYS THR SEQRES 5 A 233 THR GLY LYS LEU PRO VAL PRO TRP PRO THR LEU VAL THR SEQRES 6 A 233 THR PHE CR2 VAL GLN CYS PHE ALA ARG TYR PRO ASP HIS SEQRES 7 A 233 MET LYS GLN HIS ASP PHE PHE LYS SER ALA MET PRO GLU SEQRES 8 A 233 GLY TYR VAL GLN GLU ARG THR ILE PHE PHE LYS ASP ASP SEQRES 9 A 233 GLY ASN TYR LYS THR ARG ALA GLU VAL LYS PHE GLU GLY SEQRES 10 A 233 ASP THR LEU VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP SEQRES 11 A 233 PHE LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU SEQRES 12 A 233 TYR ASN TYR ASN SER HIS ASN VAL TYR ILE MET ALA ASP SEQRES 13 A 233 LYS GLN LYS ASN GLY ILE LYS VAL ASN PHE LYS ILE ARG SEQRES 14 A 233 HIS ASN ILE GLU ASP GLY SER VAL GLN LEU ALA ASP HIS SEQRES 15 A 233 TYR GLN GLN ASN THR PRO ILE GLY ASP GLY PRO VAL LEU SEQRES 16 A 233 LEU PRO ASP ASN HIS TYR LEU SER THR GLN SER ALA LEU SEQRES 17 A 233 SER LYS ASP PRO ASN GLU LYS ARG ASP HIS MET VAL LEU SEQRES 18 A 233 LEU GLU PHE VAL THR ALA ALA GLY ILE THR GLY SER SEQRES 1 B 271 GLY SER HIS MET SER LYS GLY GLU GLU LEU PHE THR GLY SEQRES 2 B 271 VAL VAL PRO ILE LEU VAL GLU LEU ASP GLY ASP VAL ASN SEQRES 3 B 271 GLY HIS LYS PHE SER VAL SER GLY GLU GLY GLU GLY ASP SEQRES 4 B 271 ALA THR TYR GLY LYS LEU THR LEU LYS PHE ILE CYS THR SEQRES 5 B 271 THR GLY LYS LEU PRO VAL PRO TRP PRO THR LEU VAL THR SEQRES 6 B 271 THR PHE CR2 VAL GLN CYS PHE ALA ARG TYR PRO ASP HIS SEQRES 7 B 271 MET LYS GLN HIS ASP PHE PHE LYS SER ALA MET PRO GLU SEQRES 8 B 271 GLY TYR VAL GLN GLU ARG THR ILE PHE PHE LYS ASP ASP SEQRES 9 B 271 GLY ASN TYR LYS THR ARG ALA GLU VAL LYS PHE GLU GLY SEQRES 10 B 271 ASP THR LEU VAL ASN ARG ILE GLU LEU LYS GLY ILE ASP SEQRES 11 B 271 PHE LYS GLU ASP GLY ASN ILE LEU GLY HIS LYS LEU GLU SEQRES 12 B 271 TYR ASN TYR ASN SER HIS ASN VAL TYR ILE MET ALA ASP SEQRES 13 B 271 LYS GLN LYS ASN GLY ILE LYS VAL ASN PHE LYS ILE ARG SEQRES 14 B 271 HIS ASN ILE GLU ASP GLY SER VAL GLN LEU ALA ASP HIS SEQRES 15 B 271 TYR GLN GLN ASN THR PRO ILE GLY ASP GLY PRO VAL LEU SEQRES 16 B 271 LEU PRO ASP ASN HIS TYR LEU SER THR GLN SER ALA LEU SEQRES 17 B 271 SER LYS ASP PRO ASN GLU LYS ARG ASP HIS MET VAL LEU SEQRES 18 B 271 LEU GLU PHE VAL THR ALA ALA GLY ILE THR GLY SER ASP SEQRES 19 B 271 PRO PHE LEU SER GLN LEU HIS GLN VAL GLN CYS PRO VAL SEQRES 20 B 271 CYS GLN GLN MET MET PRO ALA ALA HIS ILE ASN SER HIS SEQRES 21 B 271 LEU ASP ARG CYS LEU LEU LEU HIS PRO ALA GLY SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY MODRES 3VHT CR2 A 66 GLY MODRES 3VHT CR2 A 66 TYR MODRES 3VHT CR2 A 66 GLY MODRES 3VHT CR2 B 66 GLY MODRES 3VHT CR2 B 66 TYR MODRES 3VHT CR2 B 66 GLY HET CR2 A 66 19 HET CR2 B 66 19 HET ZN B 401 1 HETNAM CR2 {(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]- HETNAM 2 CR2 5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID HETNAM ZN ZINC ION HETSYN CR2 CHROMOPHORE (GLY-TYR-GLY) FORMUL 1 CR2 2(C13 H13 N3 O4) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *133(H2 O) HELIX 1 1 SER A 2 LEU A 7 1 6 HELIX 2 2 PRO A 56 VAL A 61 5 6 HELIX 3 3 VAL A 68 ALA A 72 5 5 HELIX 4 4 PRO A 75 HIS A 81 5 7 HELIX 5 5 ASP A 82 ALA A 87 1 6 HELIX 6 6 LYS A 156 ASN A 159 5 4 HELIX 7 7 LYS B 3 THR B 9 5 7 HELIX 8 8 PRO B 56 VAL B 61 5 6 HELIX 9 9 VAL B 68 ALA B 72 5 5 HELIX 10 10 PRO B 75 HIS B 81 5 7 HELIX 11 11 ASP B 82 ALA B 87 1 6 HELIX 12 12 LYS B 156 ASN B 159 5 4 HELIX 13 13 HIS B 255 HIS B 267 1 13 HELIX 14 14 THR C 22 GLY C 35 1 14 HELIX 15 15 PRO C 37 ASP C 39 5 3 SHEET 1 A12 VAL A 11 VAL A 22 0 SHEET 2 A12 HIS A 25 ASP A 36 -1 O PHE A 27 N GLY A 20 SHEET 3 A12 LYS A 41 CYS A 48 -1 O THR A 43 N GLU A 34 SHEET 4 A12 HIS A 217 ALA A 227 -1 O LEU A 220 N LEU A 44 SHEET 5 A12 HIS A 199 SER A 208 -1 N SER A 202 O THR A 225 SHEET 6 A12 HIS A 148 ASP A 155 -1 N ILE A 152 O HIS A 199 SHEET 7 A12 GLY A 160 ASN A 170 -1 O GLY A 160 N ASP A 155 SHEET 8 A12 VAL A 176 PRO A 187 -1 O HIS A 181 N PHE A 165 SHEET 9 A12 TYR A 92 PHE A 100 -1 N VAL A 93 O THR A 186 SHEET 10 A12 ASN A 105 GLU A 115 -1 O ALA A 110 N GLN A 94 SHEET 11 A12 THR A 118 ILE A 128 -1 O GLU A 124 N ARG A 109 SHEET 12 A12 VAL A 11 VAL A 22 1 N ASP A 21 O GLY A 127 SHEET 1 B12 VAL B 12 VAL B 22 0 SHEET 2 B12 HIS B 25 GLY B 35 -1 O GLY B 33 N ILE B 14 SHEET 3 B12 LYS B 41 CYS B 48 -1 O ILE B 47 N SER B 30 SHEET 4 B12 HIS B 217 ALA B 227 -1 O LEU B 220 N LEU B 44 SHEET 5 B12 HIS B 199 SER B 208 -1 N SER B 202 O THR B 225 SHEET 6 B12 HIS B 148 ASP B 155 -1 N HIS B 148 O THR B 203 SHEET 7 B12 GLY B 160 ASN B 170 -1 O LYS B 162 N MET B 153 SHEET 8 B12 VAL B 176 PRO B 187 -1 O HIS B 181 N PHE B 165 SHEET 9 B12 TYR B 92 PHE B 100 -1 N VAL B 93 O THR B 186 SHEET 10 B12 ASN B 105 GLU B 115 -1 O TYR B 106 N ILE B 98 SHEET 11 B12 THR B 118 ILE B 128 -1 O THR B 118 N GLU B 115 SHEET 12 B12 VAL B 12 VAL B 22 1 N ASP B 21 O GLY B 127 SHEET 1 C 2 GLN B 241 GLN B 243 0 SHEET 2 C 2 MET B 250 PRO B 252 -1 O MET B 251 N VAL B 242 SHEET 1 D 5 THR C 12 GLU C 16 0 SHEET 2 D 5 GLN C 2 THR C 7 -1 N ILE C 3 O LEU C 15 SHEET 3 D 5 THR C 66 LEU C 71 1 O LEU C 67 N LYS C 6 SHEET 4 D 5 GLN C 41 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 D 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 LINK C PHE A 64 N1 CR2 A 66 1555 1555 1.32 LINK C3 CR2 A 66 N VAL A 68 1555 1555 1.27 LINK C PHE B 64 N1 CR2 B 66 1555 1555 1.29 LINK C3 CR2 B 66 N VAL B 68 1555 1555 1.27 LINK SG CYS B 244 ZN ZN B 401 1555 1555 2.30 LINK SG CYS B 247 ZN ZN B 401 1555 1555 2.36 LINK NE2 HIS B 259 ZN ZN B 401 1555 1555 1.83 LINK SG CYS B 263 ZN ZN B 401 1555 1555 2.26 CISPEP 1 MET A 88 PRO A 89 0 6.56 CISPEP 2 MET B 88 PRO B 89 0 5.42 SITE 1 AC1 4 CYS B 244 CYS B 247 HIS B 259 CYS B 263 CRYST1 88.950 143.692 106.864 90.00 90.00 90.00 C 2 2 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 0.011242 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006959 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009358 0.00000