PDB Short entry for 3BJ9 HEADER IMMUNE SYSTEM 03-DEC-07 3BJ9 TITLE CRYSTAL STRUCTURE OF THE SURROGATE LIGHT CHAIN VARIABLE DOMAIN VPREBJ COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN IOTA CHAIN, IMMUNOGLOBULIN LAMBDA-LIKE COMPND 3 POLYPEPTIDE 1; COMPND 4 CHAIN: 1; COMPND 5 FRAGMENT: FUSION PROTEIN CONSISTS OF IG DOMAIN OF VPREB PROTEIN AND COMPND 6 J-FRAGMENT OF IG LAMBDA-5; COMPND 7 SYNONYM: VPRE, B PROTEIN, VPREB PROTEIN, CD179A ANTIGEN, COMPND 8 IMMUNOGLOBULIN-RELATED PROTEIN 14.1, IMMUNOGLOBULIN OMEGA COMPND 9 POLYPEPTIDE, IG LAMBDA-5, CD179B ANTIGEN; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VPREB1, VPREB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE)PLYSE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PIG203 KEYWDS IMMUNOGLOBULIN DOMAIN, BETA SHEET, POLYMORPHISM, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.M.MORSTADT,A.A.BOHM,B.D.STOLLAR,J.D.BALEJA REVDAT 4 04-SEP-19 3BJ9 1 REMARK REVDAT 3 04-APR-18 3BJ9 1 REMARK REVDAT 2 24-FEB-09 3BJ9 1 VERSN REVDAT 1 04-MAR-08 3BJ9 0 JRNL AUTH L.MORSTADT,A.BOHM,D.YUKSEL,K.KUMAR,B.D.STOLLAR,J.D.BALEJA JRNL TITL ENGINEERING AND CHARACTERIZATION OF A SINGLE CHAIN SURROGATE JRNL TITL 2 LIGHT CHAIN VARIABLE DOMAIN. JRNL REF PROTEIN SCI. V. 17 458 2008 JRNL REFN ISSN 0961-8368 JRNL PMID 18287279 JRNL DOI 10.1110/PS.073269808 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9712 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 519 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 635 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.1830 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.2370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 909 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.03000 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): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.250 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1000 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1361 ; 1.622 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 129 ;15.567 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;31.453 ;22.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 158 ;14.724 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;12.762 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 141 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 792 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 438 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 655 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 110 ; 0.197 ; 0.200 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): 50 ; 0.281 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.179 ; 0.200 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): 632 ; 0.831 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 989 ; 1.344 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 425 ; 1.754 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 368 ; 2.544 ; 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 : 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 REMARK 4 REMARK 4 3BJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9712 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 55.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE, 1M SODIUM ACETATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 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 0.00000 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 21.90550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.58800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.91500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 21.90550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.58800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.91500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 21.90550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.58800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.91500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 21.90550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.58800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.91500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 1 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 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 ARG 1 101 NH2 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 NE2 GLN 1 87 OE1 GLU 1 89 2.08 REMARK 500 O HOH 1 140 O HOH 1 230 2.09 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 THR 1 23 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 ASP 1 27 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP 1 73 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG 1 101 NH1 - CZ - NH2 ANGL. DEV. = 19.1 DEGREES REMARK 500 ARG 1 101 NE - CZ - NH2 ANGL. DEV. = -18.6 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 1 26 7.08 -167.47 REMARK 500 ASN 1 26 8.40 -167.47 REMARK 500 ALA 1 92 174.69 178.60 REMARK 500 ARG 1 101 -97.82 114.62 REMARK 500 SER 1 102 -76.93 70.04 REMARK 500 SER 1 102 -76.93 78.63 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 CYS 1 22 THR 1 23 -140.23 REMARK 500 ALA 1 100 ARG 1 101 -132.02 REMARK 500 ARG 1 101 SER 1 102 53.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO 1 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO 1 119 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO 1 120 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE 14 RESIDUES: THVFGSGTQLTVLS BELONG TO THE "J-SEGMENT, FUSED REMARK 999 TO THE IG DOMAIN OF VPREB" DBREF 3BJ9 1 3 102 UNP P12018 VPREB_HUMAN 22 121 SEQADV 3BJ9 THR 1 103 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 HIS 1 104 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 VAL 1 105 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 PHE 1 106 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 GLY 1 107 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 GLY 1 109 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 THR 1 110 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 GLN 1 111 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 LEU 1 112 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 THR 1 113 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 VAL 1 114 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 LEU 1 115 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 SER 1 116 UNP P12018 SEE REMARK 999 SEQADV 3BJ9 ALA 1 117 UNP P12018 EXPRESSION TAG SEQADV 3BJ9 ALA 1 118 UNP P12018 EXPRESSION TAG SEQRES 1 1 116 VAL LEU HIS GLN PRO PRO ALA MET SER SER ALA LEU GLY SEQRES 2 1 116 THR THR ILE ARG LEU THR CYS THR LEU ARG ASN ASP HIS SEQRES 3 1 116 ASP ILE GLY VAL TYR SER VAL TYR TRP TYR GLN GLN ARG SEQRES 4 1 116 PRO GLY HIS PRO PRO ARG PHE LEU LEU ARG TYR PHE SER SEQRES 5 1 116 GLN SER ASP LYS SER GLN GLY PRO GLN VAL PRO PRO ARG SEQRES 6 1 116 PHE SER GLY SER LYS ASP VAL ALA ARG ASN ARG GLY TYR SEQRES 7 1 116 LEU SER ILE SER GLU LEU GLN PRO GLU ASP GLU ALA MET SEQRES 8 1 116 TYR TYR CYS ALA MET GLY ALA ARG SER THR HIS VAL PHE SEQRES 9 1 116 GLY SER GLY THR GLN LEU THR VAL LEU SER ALA ALA HET EDO 1 1 4 HET EDO 1 119 4 HET EDO 1 120 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 3(C2 H6 O2) FORMUL 5 HOH *111(H2 O) HELIX 1 1 ASP 1 29 TYR 1 33 5 5 HELIX 2 2 VAL 1 74 ARG 1 76 5 3 HELIX 3 3 GLN 1 87 GLU 1 91 5 5 SHEET 1 A 4 LEU 1 4 HIS 1 5 0 SHEET 2 A 4 ILE 1 18 LEU 1 24 -1 O THR 1 23 N HIS 1 5 SHEET 3 A 4 ARG 1 78 ILE 1 83 -1 O LEU 1 81 N LEU 1 20 SHEET 4 A 4 PHE 1 68 ASP 1 73 -1 N SER 1 69 O SER 1 82 SHEET 1 B 6 ALA 1 9 ALA 1 13 0 SHEET 2 B 6 THR 1 110 LEU 1 115 1 O LEU 1 115 N SER 1 12 SHEET 3 B 6 ALA 1 92 MET 1 98 -1 N ALA 1 92 O LEU 1 112 SHEET 4 B 6 VAL 1 35 GLN 1 40 -1 N TYR 1 36 O ALA 1 97 SHEET 5 B 6 ARG 1 47 SER 1 54 -1 O TYR 1 52 N VAL 1 35 SHEET 6 B 6 ASP 1 57 GLN 1 60 -1 O SER 1 59 N ARG 1 51 SHEET 1 C 4 ALA 1 9 ALA 1 13 0 SHEET 2 C 4 THR 1 110 LEU 1 115 1 O LEU 1 115 N SER 1 12 SHEET 3 C 4 ALA 1 92 MET 1 98 -1 N ALA 1 92 O LEU 1 112 SHEET 4 C 4 VAL 1 105 PHE 1 106 -1 O VAL 1 105 N MET 1 98 SSBOND 1 CYS 1 22 CYS 1 96 1555 1555 2.02 CISPEP 1 ARG 1 25 ASN 1 26 0 -17.32 CISPEP 2 ARG 1 101 SER 1 102 0 -23.23 SITE 1 AC1 4 GLN 1 60 GLY 1 61 HOH 1 180 HOH 1 205 SITE 1 AC2 6 GLN 1 39 ARG 1 47 PRO 1 65 HOH 1 136 SITE 2 AC2 6 HOH 1 201 HOH 1 224 SITE 1 AC3 5 PRO 1 8 SER 1 108 GLY 1 109 HOH 1 199 SITE 2 AC3 5 HOH 1 231 CRYST1 43.811 67.176 99.830 90.00 90.00 90.00 I 2 2 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 0.022825 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014886 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010017 0.00000